rs3743979
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001243279.3(ACSF3):c.1114G>A(p.Val372Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 1,612,188 control chromosomes in the GnomAD database, including 436,948 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001243279.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.707 AC: 107453AN: 151950Hom.: 38462 Cov.: 32
GnomAD3 exomes AF: 0.716 AC: 178900AN: 249890Hom.: 65253 AF XY: 0.712 AC XY: 96431AN XY: 135342
GnomAD4 exome AF: 0.736 AC: 1074531AN: 1460120Hom.: 398474 Cov.: 79 AF XY: 0.733 AC XY: 532654AN XY: 726510
GnomAD4 genome AF: 0.707 AC: 107494AN: 152068Hom.: 38474 Cov.: 32 AF XY: 0.705 AC XY: 52435AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Combined malonic and methylmalonic acidemia Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 03, 2025 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Methylmalonic acidemia Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 01, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at