20-3854664-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001206491.2(MAVS):c.-209C>T variant causes a 5 prime UTR premature start codon gain 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001206491.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAVS | ENST00000416600 | c.-209C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 6 | 1 | ENSP00000413749.2 | ||||
MAVS | ENST00000428216.4 | c.40C>T | p.Arg14Cys | missense_variant | Exon 2 of 7 | 1 | NM_020746.5 | ENSP00000401980.2 | ||
MAVS | ENST00000416600 | c.-209C>T | 5_prime_UTR_variant | Exon 2 of 6 | 1 | ENSP00000413749.2 |
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
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