rs12329760
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005656.4(TMPRSS2):c.478G>A(p.Val160Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,613,468 control chromosomes in the GnomAD database, including 47,374 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005656.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMPRSS2 | NM_005656.4 | c.478G>A | p.Val160Met | missense_variant | 6/14 | ENST00000332149.10 | |
TMPRSS2 | NM_001135099.1 | c.589G>A | p.Val197Met | missense_variant | 6/14 | ||
TMPRSS2 | NM_001382720.1 | c.478G>A | p.Val160Met | missense_variant | 6/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMPRSS2 | ENST00000332149.10 | c.478G>A | p.Val160Met | missense_variant | 6/14 | 1 | NM_005656.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.252 AC: 38327AN: 152004Hom.: 5298 Cov.: 33
GnomAD3 exomes AF: 0.245 AC: 61407AN: 250738Hom.: 8263 AF XY: 0.244 AC XY: 33153AN XY: 135764
GnomAD4 exome AF: 0.234 AC: 342061AN: 1461346Hom.: 42067 Cov.: 39 AF XY: 0.234 AC XY: 170309AN XY: 726950
GnomAD4 genome ? AF: 0.252 AC: 38372AN: 152122Hom.: 5307 Cov.: 33 AF XY: 0.259 AC XY: 19230AN XY: 74384
ClinVar
Submissions by phenotype
Associated with severe COVID-19 disease Uncertain:1
Uncertain significance, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Jul 01, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 26, 2021 | This variant is associated with the following publications: (PMID: 32867305) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at