chr20-3865791-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020746.5(MAVS):c.1267G>A(p.Val423Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,613,814 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 Likely benign (★).
Frequency
Consequence
NM_020746.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAVS | NM_020746.5 | c.1267G>A | p.Val423Met | missense_variant | 7/7 | ENST00000428216.4 | |
MAVS | NM_001206491.2 | c.844G>A | p.Val282Met | missense_variant | 6/6 | ||
MAVS | NM_001385663.1 | c.844G>A | p.Val282Met | missense_variant | 8/8 | ||
MAVS | NR_037921.2 | n.1231G>A | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAVS | ENST00000428216.4 | c.1267G>A | p.Val423Met | missense_variant | 7/7 | 1 | NM_020746.5 | P1 | |
MAVS | ENST00000416600.6 | c.844G>A | p.Val282Met | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250828Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135786
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461528Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 49AN XY: 727082
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at