20-3854664-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020746.5(MAVS):c.40C>T(p.Arg14Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,766 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R14H) has been classified as Likely benign.
Frequency
Consequence
NM_020746.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAVS | NM_020746.5 | c.40C>T | p.Arg14Cys | missense_variant | 2/7 | ENST00000428216.4 | |
MAVS | NM_001206491.2 | c.-209C>T | 5_prime_UTR_variant | 2/6 | |||
MAVS | NM_001385663.1 | c.-508C>T | 5_prime_UTR_variant | 2/8 | |||
MAVS | NR_037921.2 | n.177C>T | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAVS | ENST00000428216.4 | c.40C>T | p.Arg14Cys | missense_variant | 2/7 | 1 | NM_020746.5 | P1 | |
MAVS | ENST00000416600.6 | c.-209C>T | 5_prime_UTR_variant | 2/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152024Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251448Hom.: 1 AF XY: 0.0000736 AC XY: 10AN XY: 135894
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461742Hom.: 1 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727164
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152024Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74240
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.40C>T (p.R14C) alteration is located in exon 2 (coding exon 1) of the MAVS gene. This alteration results from a C to T substitution at nucleotide position 40, causing the arginine (R) at amino acid position 14 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at