4-6301030-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_006005.3(WFS1):c.1235T>C(p.Val412Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000261 in 1,614,094 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V412L) has been classified as Likely benign.
Frequency
Consequence
NM_006005.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WFS1 | NM_006005.3 | c.1235T>C | p.Val412Ala | missense_variant | 8/8 | ENST00000226760.5 | |
WFS1 | NM_001145853.1 | c.1235T>C | p.Val412Ala | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WFS1 | ENST00000226760.5 | c.1235T>C | p.Val412Ala | missense_variant | 8/8 | 1 | NM_006005.3 | P2 | |
ENST00000661896.1 | n.1337+2885A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152108Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000700 AC: 176AN: 251480Hom.: 1 AF XY: 0.000625 AC XY: 85AN XY: 135914
GnomAD4 exome AF: 0.000259 AC: 379AN: 1461868Hom.: 1 Cov.: 104 AF XY: 0.000259 AC XY: 188AN XY: 727240
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.000417 AC XY: 31AN XY: 74418
ClinVar
Submissions by phenotype
Autosomal dominant nonsyndromic hearing loss 6 Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Wolfram syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 06, 2018 | The p.Val412Ala variant in WFS1 has been reported in several studies in associat ion with hearing loss, diabetes, and goiter (Fukouka 2007, Yan 2013, Awata 2013, Choi 2013, Li 2016) but has also been identified in 0.92% (173/18864) of East A sian chromosomes, including 1 homozygote, by the Genome Aggregation Database (ht tp://gnomad.broadinstitute.org). Therefore, this variant is classified as benign for hearing loss. ACMG/AMP criteria applied: PP3, BA1. - |
WFS1-Related Spectrum Disorders Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at