This variant may be annotated on the current canonical isoform (NM_000492.4) using the following expression,
directly in the search engine at the bottom of the page or by using the blue button below:
NC_000007.14:g.117664795_117664797delinsAA;CFTR
Try annotation on the canonical NM_000492.4 Annotating the variant on NM_000492.4
Nomenclatures
Features | Values | Descriptions |
---|---|---|
HGNC gene symbol (ID): | CFTR (1884) | HGNC gene symbol and corresponding ID |
HGVS DNA on transcript: |
NM_000492.3:c.4071_4073delinsAA
RefSeq Select
|
HGVS full nomenclature at DNA level on transcript |
HGVS RNA: | r.(?) | HGVS full nomenclature at RNA level |
HGVS Protein: | NP_000483.3:p.(Arg1358AsnfsTer22) | HGVS full nomenclature at protein level |
HGVS genomic (hg19): | chr7(hg19):g.117304849_117304851delinsAA | HGVS full nomenclature at genomic level (hg19) |
HGVS strict genomic (hg19): | NC_000007.13:g.117304849_117304851delinsAA | HGVS full strict nomenclature at genomic level (hg19) |
pseudo VCF (hg19): | hg19-7-117304849-TAG-AA | chr-pos-ref-alt (hg19) |
HGVS genomic (hg38): | chr7(hg38):g.117664795_117664797delinsAA | HGVS full nomenclature at genomic level (hg38) |
HGVS strict genomic (hg38): | NC_000007.14:g.117664795_117664797delinsAA | HGVS full strict nomenclature at genomic level (hg38) |
pseudo VCF (hg38): | hg38-7-117664795-TAG-AA | chr-pos-ref-alt (hg38) |
Positions
Features | Values | Descriptions |
---|---|---|
Position in transcript: | Exon 25 | Exon/intron position in NM_000492.3 |
Position / splice site | 66 bp from donor | Position relative to the nearest splice site |
Position / protein | 1358 / 1479 | Position relative to the protein |
Position / domain | ABC transporter 2 (1210 - 1443) | Position in a protein domain (UNIPROT: P13569) |
Wild type sequence | GCCACAAGCAGTTGATGTGCTTGGC TAG ATCTGTTCTCAGTAAGGCGAAGATC | Wild type DNA sequence +/- 25 bp |
Mutant sequence | GCCACAAGCAGTTGATGTGCTTGGC AA- ATCTGTTCTCAGTAAGGCGAAGATC | Mutant DNA sequence +/- 25 bp |
Population Frequencies and Databases
Features | Values | Descriptions |
---|---|---|
gnomAD exome: | No match in gnomAD exome | v2.1.1 Exomes global MAF |
gnomAD genome: | No match in gnomAD genome | v2.1.1 Genomes global MAF |
gnomAD exome (non cancer): | No match in gnomAD exome | v2.1.1 Exomes MAX MAF for non-cancer dataset |
gnomAD v4 Genome: | No match in gnomADv4 Genome | v4.1.0 Genomes global MAF |
gnomAD v4 Exome: | No match in gnomADv4 Exome | v4.1.0 Exomes global MAF |
dbSNP rsid: | No match in dbSNP v156 | Identifier for NCBI dbSNP |
Clinvar Germline: | Pathogenic * | Clinvar interpretation |
ClinGen EvRepo: | Searching for ClinGen EvRepo data... | ClinGen Evidence Repository Classification for the variant |
GeneBe: | Asking GeneBe... | Semi-automated ACMG classification - click on the GeneBe link to adjust - passing the mouse over a criterion will display the definition |
LOVD matches: | Searching LOVD... | LOVD match in public instances |
exon indel +
Overall predictions
Features | Values | Descriptions |
---|---|---|
CADD raw: | No match in CADD v1.6 | [-6.41;35.5] The higher the less likely to be observed |
CADD phred: | No match in CADD v1.6 | Phred-like scaling of raw score |
Eigen raw: | None | [-3.33;6.84] The higher the less likely to be observed |
Eigen phred: | None | Phred-like scaling of raw score |
MPA score: | 10 | Raw score [0;10], 10: high impact |
MPA impact: | Clinvar pathogenic | Impact type |
Splicing predictions
Exonic context
The exonic splicing context of the variant including natural splice sites scores is summarized in the graph below:
MaxEntScan results
MaxEntScan scores are presented in the two following tables. Selected scores have:
- a |variation| > 15% and
- a raw score for mutant or wild-type of at least 3
Wild-type sequence | Score | Mutant sequence | Score | Variation(%) |
---|---|---|---|---|
... CTCAGTAAG
... ... CTCagtaag ... |
-36.61 | ... TCAGTAAGG
... ... TCAgtaagg ... |
5.20 | +114.2 |
... TCAGTAAGG
... ... TCAgtaagg ... |
5.20 | ... CAGTAAGGC
... ... CAGtaaggc ... |
-6.81 | -230.96 |
Wild-type sequence | Score | Mutant sequence | Score | Variation(%) |
---|---|---|---|---|
No MaxEnt 3'ss score performed (exonic variant far form 3'ss). |
SPiP results
SPiP results and predictions:
MobiDetails is running SPiPv2 (may last up to 20s)...
SpliceAI-visual results
SpliceAI-visual displays SpliceAI raw (absolute) predictions:
- Green and red highlights show the variation site on the wild-type and mutant track, respectively
- Positive orange bars represent predicted acceptor sites ([0;1]), and negative blue bars donor sites ([-1;0]), the spliceai raw score being the absolute value.
- The first track is the spliceai prediction for the entire MANE transcript.
- The second track is the prediction for the variant, +/- 10kb inside the transcript (i.e. not considering intergenic nucleotides).
- The "inserted nucleotides" track is used to display the scores of the nucleotides being part of the insertion (empty if no insertion)
- You can download the Wild-type and mutant bedgraphs in order to load them in your own Desktop IGV or the UCSC genome browser.
- Important notice: if your intronic variant is located more than 10kb from one of the two flanking exons, you are advised to click on the "SpliceAI-visual full transcript" button at the top of this text. Depending on the size of your transcript, within 30s-10 minutes (for the DMD gene, the bad news), the whole transcript prediction including the variant will appear as a new track in the igv.js browser, allowing a more accurate prediction for your variant. The good news being that if it has already been computed, it will load automatically.
- How to cite?
MobiDetails is running spliceai to bring you SpliceAI-visual...
Classification History
Variant | User | Date | ACMG Classification* | Comments |
---|---|---|---|---|
NM_000492.3(CFTR):c.4071_4073delinsAA
Current
|
CFTR-France | 2022-10-06 | Class 5 (pathogenic) |
To modify the classification history, you must be logged in (you might want to create an account before).
* We added an additional 'risk factor' class to the 5 ACMG classes in order to describe low penetrance risk factor variants. Currently, these variants are not sent to the LOVD Global Variome instance.
Administrative information
Features | Values | Descriptions |
---|---|---|
Creation user: | CFTR-France | User who created the variant |
Creation date: | 2021-01-12 | Date of creation in MD |
mobidetails
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