chr3-13818966-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP6BS1
The NM_004625.4(WNT7A):c.1028C>T(p.Thr343Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,588,138 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T343T) has been classified as Likely benign.
Frequency
Consequence
NM_004625.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT7A | NM_004625.4 | c.1028C>T | p.Thr343Met | missense_variant | 4/4 | ENST00000285018.5 | |
WNT7A | XM_011534091.3 | c.827C>T | p.Thr276Met | missense_variant | 5/5 | ||
WNT7A | XM_047448863.1 | c.827C>T | p.Thr276Met | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT7A | ENST00000285018.5 | c.1028C>T | p.Thr343Met | missense_variant | 4/4 | 1 | NM_004625.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000394 AC: 60AN: 152248Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000218 AC: 52AN: 238408Hom.: 0 AF XY: 0.000188 AC XY: 24AN XY: 127972
GnomAD4 exome AF: 0.000121 AC: 174AN: 1435890Hom.: 0 Cov.: 30 AF XY: 0.000100 AC XY: 71AN XY: 709636
GnomAD4 genome ? AF: 0.000394 AC: 60AN: 152248Hom.: 1 Cov.: 32 AF XY: 0.000444 AC XY: 33AN XY: 74384
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 01, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 14, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at