rs13440436
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001366145.2(TRPM3):c.4919C>T(p.Thr1640Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00203 in 1,614,230 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001366145.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRPM3 | NM_001366145.2 | c.4919C>T | p.Thr1640Ile | missense_variant | Exon 26 of 26 | ENST00000677713.2 | NP_001353074.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRPM3 | ENST00000677713.2 | c.4919C>T | p.Thr1640Ile | missense_variant | Exon 26 of 26 | NM_001366145.2 | ENSP00000503830.2 |
Frequencies
GnomAD3 genomes AF: 0.0111 AC: 1683AN: 152222Hom.: 33 Cov.: 32
GnomAD3 exomes AF: 0.00278 AC: 698AN: 251470Hom.: 11 AF XY: 0.00191 AC XY: 259AN XY: 135900
GnomAD4 exome AF: 0.00108 AC: 1584AN: 1461890Hom.: 31 Cov.: 82 AF XY: 0.000924 AC XY: 672AN XY: 727244
GnomAD4 genome AF: 0.0111 AC: 1685AN: 152340Hom.: 33 Cov.: 32 AF XY: 0.0112 AC XY: 832AN XY: 74496
ClinVar
Submissions by phenotype
TRPM3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at