chr21-37240615-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_006052.2(VPS26C):āc.82A>Gā(p.Ile28Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,614,134 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006052.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00129 AC: 197AN: 152204Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000330 AC: 83AN: 251214Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135796
GnomAD4 exome AF: 0.000170 AC: 249AN: 1461812Hom.: 1 Cov.: 31 AF XY: 0.000149 AC XY: 108AN XY: 727212
GnomAD4 genome AF: 0.00129 AC: 197AN: 152322Hom.: 1 Cov.: 32 AF XY: 0.00121 AC XY: 90AN XY: 74478
ClinVar
Submissions by phenotype
VPS26C-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 24, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at