chr4-6301980-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_006005.3(WFS1):c.2185G>A(p.Asp729Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000763 in 1,612,746 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). Synonymous variant affecting the same amino acid position (i.e. D729D) 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WFS1 | NM_006005.3 | c.2185G>A | p.Asp729Asn | missense_variant | 8/8 | ENST00000226760.5 | |
WFS1 | NM_001145853.1 | c.2185G>A | p.Asp729Asn | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WFS1 | ENST00000226760.5 | c.2185G>A | p.Asp729Asn | missense_variant | 8/8 | 1 | NM_006005.3 | P2 | |
ENST00000661896.1 | n.1337+1935C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152226Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000105 AC: 26AN: 246912Hom.: 0 AF XY: 0.000164 AC XY: 22AN XY: 134444
GnomAD4 exome AF: 0.0000781 AC: 114AN: 1460402Hom.: 1 Cov.: 98 AF XY: 0.000116 AC XY: 84AN XY: 726490
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152344Hom.: 0 Cov.: 34 AF XY: 0.0000537 AC XY: 4AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 30, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at