rs199959383
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_015910.7(WDPCP):c.985G>A(p.Val329Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,613,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_015910.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDPCP | NM_015910.7 | c.985G>A | p.Val329Met | missense_variant | 10/18 | ENST00000272321.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDPCP | ENST00000272321.12 | c.985G>A | p.Val329Met | missense_variant | 10/18 | 1 | NM_015910.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00137 AC: 209AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00115 AC: 287AN: 249068Hom.: 1 AF XY: 0.00113 AC XY: 153AN XY: 135116
GnomAD4 exome AF: 0.00113 AC: 1653AN: 1461718Hom.: 0 Cov.: 31 AF XY: 0.00106 AC XY: 770AN XY: 727146
GnomAD4 genome ? AF: 0.00137 AC: 209AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.00180 AC XY: 134AN XY: 74450
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 15 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 11, 2016 | - - |
Bardet-Biedl syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at