rs3986599
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014555.4(TRPM5):āc.761T>Cā(p.Val254Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 1,568,652 control chromosomes in the GnomAD database, including 376,855 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014555.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRPM5 | NM_014555.4 | c.761T>C | p.Val254Ala | missense_variant | 11/29 | ENST00000696290.1 | NP_055370.1 | |
TRPM5 | XM_017017628.2 | c.815T>C | p.Val272Ala | missense_variant | 8/26 | XP_016873117.1 | ||
TRPM5 | XM_047426858.1 | c.815T>C | p.Val272Ala | missense_variant | 8/26 | XP_047282814.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRPM5 | ENST00000696290.1 | c.761T>C | p.Val254Ala | missense_variant | 11/29 | NM_014555.4 | ENSP00000512529 | P2 | ||
TRPM5 | ENST00000533060.5 | c.761T>C | p.Val254Ala | missense_variant | 6/24 | 1 | ENSP00000434121 | A2 | ||
TRPM5 | ENST00000528453.1 | c.761T>C | p.Val254Ala | missense_variant | 6/24 | 1 | ENSP00000436809 | A2 | ||
TRPM5 | ENST00000533881.5 | c.743T>C | p.Val248Ala | missense_variant | 6/24 | 1 | ENSP00000434383 |
Frequencies
GnomAD3 genomes AF: 0.760 AC: 115289AN: 151730Hom.: 44939 Cov.: 31
GnomAD3 exomes AF: 0.738 AC: 133451AN: 180908Hom.: 50177 AF XY: 0.732 AC XY: 71237AN XY: 97342
GnomAD4 exome AF: 0.681 AC: 964449AN: 1416804Hom.: 331857 Cov.: 71 AF XY: 0.682 AC XY: 477741AN XY: 700460
GnomAD4 genome AF: 0.760 AC: 115408AN: 151848Hom.: 44998 Cov.: 31 AF XY: 0.761 AC XY: 56460AN XY: 74174
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at