11-117904080-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001077263.3(TMPRSS13):c.1403G>A(p.Arg468Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000695 in 1,614,042 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001077263.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMPRSS13 | NM_001077263.3 | c.1403G>A | p.Arg468Gln | missense_variant | Exon 11 of 13 | ENST00000524993.6 | NP_001070731.1 | |
TMPRSS13 | NM_001244995.2 | c.1403G>A | p.Arg468Gln | missense_variant | Exon 11 of 13 | NP_001231924.1 | ||
TMPRSS13 | NM_001206789.2 | c.1298G>A | p.Arg433Gln | missense_variant | Exon 10 of 12 | NP_001193718.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMPRSS13 | ENST00000524993.6 | c.1403G>A | p.Arg468Gln | missense_variant | Exon 11 of 13 | 1 | NM_001077263.3 | ENSP00000434279.1 | ||
TMPRSS13 | ENST00000445164.6 | c.1403G>A | p.Arg468Gln | missense_variant | Exon 11 of 12 | 1 | ENSP00000394114.2 | |||
TMPRSS13 | ENST00000430170.6 | c.1403G>A | p.Arg468Gln | missense_variant | Exon 11 of 13 | 1 | ENSP00000387702.2 | |||
TMPRSS13 | ENST00000528626.5 | c.1298G>A | p.Arg433Gln | missense_variant | Exon 10 of 12 | 1 | ENSP00000435813.1 |
Frequencies
GnomAD3 genomes AF: 0.000506 AC: 77AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000698 AC: 174AN: 249126Hom.: 0 AF XY: 0.000651 AC XY: 88AN XY: 135142
GnomAD4 exome AF: 0.000714 AC: 1044AN: 1461730Hom.: 1 Cov.: 36 AF XY: 0.000692 AC XY: 503AN XY: 727164
GnomAD4 genome AF: 0.000506 AC: 77AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at