rs397508472
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000492.4(CFTR):c.2997_3000del(p.Ile1000Ter) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,904 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. L998L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000492.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFTR | NM_000492.4 | c.2997_3000del | p.Ile1000Ter | frameshift_variant | 19/27 | ENST00000003084.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFTR | ENST00000003084.11 | c.2997_3000del | p.Ile1000Ter | frameshift_variant | 19/27 | 1 | NM_000492.4 | P2 | |
ENST00000456270.1 | n.178-5538_178-5535del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460904Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 726784
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Cystic fibrosis Pathogenic:5
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2022 | The c.2997_3000delAATT pathogenic mutaiton, located in coding exon 19 of the CFTR gene, results from a deletion of 4 nucleotides at nucleotide positions 2997 to 3000, causing a translational frameshift with a predicted alternate stop codon (p.I1000*). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration has been detected in the homozygous state, or in conjunction with another CFTR pathogenic mutation, in multiple unrelated individuals with cystic fibrosis or CFTR-related disorders (AbdulWahab A et al. Qatar Med J, 2021 Jul;2021:24; Liu K et al. Orphanet J Rare Dis, 2020 06;15:150; El-Seedy A et al. Cell Mol Biol (Noisy-le-grand), 2016 Nov;62:21-28). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | Nov 05, 2018 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | May 11, 2016 | - - |
Pathogenic, criteria provided, single submitter | curation | CFTR-France | Jan 29, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Sep 18, 2021 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 53618). This variant is also known as 3126del4 and/or 3129del4. This premature translational stop signal has been observed in individual(s) with CFTR-related conditions (PMID: 11788090, 32539862). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ile1000*) in the CFTR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CFTR are known to be pathogenic (PMID: 1695717, 7691345, 9725922). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at