rs1129235
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_016113.5(TRPV2):āc.427A>Cā(p.Arg143=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,610,794 control chromosomes in the GnomAD database, including 125,044 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.43 ( 14879 hom., cov: 33)
Exomes š: 0.38 ( 110165 hom. )
Consequence
TRPV2
NM_016113.5 synonymous
NM_016113.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.783
Genes affected
TRPV2 (HGNC:18082): (transient receptor potential cation channel subfamily V member 2) This gene encodes an ion channel that is activated by high temperatures above 52 degrees Celsius. The protein may be involved in transduction of high-temperature heat responses in sensory ganglia. It is thought that in other tissues the channel may be activated by stimuli other than heat. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
?
Synonymous conserved (PhyloP=-0.783 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPV2 | NM_016113.5 | c.427A>C | p.Arg143= | synonymous_variant | 4/15 | ENST00000338560.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPV2 | ENST00000338560.12 | c.427A>C | p.Arg143= | synonymous_variant | 4/15 | 1 | NM_016113.5 | P1 | |
TRPV2 | ENST00000455666.1 | c.301A>C | p.Arg101= | synonymous_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.432 AC: 65704AN: 151990Hom.: 14860 Cov.: 33
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GnomAD3 exomes AF: 0.365 AC: 89580AN: 245518Hom.: 17125 AF XY: 0.358 AC XY: 47535AN XY: 132634
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GnomAD4 exome AF: 0.384 AC: 559546AN: 1458686Hom.: 110165 Cov.: 55 AF XY: 0.379 AC XY: 275241AN XY: 725316
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GnomAD4 genome ? AF: 0.432 AC: 65779AN: 152108Hom.: 14879 Cov.: 33 AF XY: 0.429 AC XY: 31933AN XY: 74354
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at