chr17-16422769-A-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016113.5(TRPV2):āc.505A>Gā(p.Ile169Val) variant causes a missense change. The variant allele was found at a frequency of 0.00011 in 1,575,176 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00020 ( 1 hom., cov: 34)
Exomes š: 0.00010 ( 0 hom. )
Consequence
TRPV2
NM_016113.5 missense
NM_016113.5 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 4.00
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.041771412).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPV2 | NM_016113.5 | c.505A>G | p.Ile169Val | missense_variant | 4/15 | ENST00000338560.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPV2 | ENST00000338560.12 | c.505A>G | p.Ile169Val | missense_variant | 4/15 | 1 | NM_016113.5 | P1 | |
TRPV2 | ENST00000455666.1 | c.379A>G | p.Ile127Val | missense_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152258Hom.: 1 Cov.: 34
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GnomAD3 exomes AF: 0.000236 AC: 44AN: 186720Hom.: 0 AF XY: 0.000171 AC XY: 17AN XY: 99638
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GnomAD4 exome AF: 0.000101 AC: 143AN: 1422800Hom.: 0 Cov.: 36 AF XY: 0.0000980 AC XY: 69AN XY: 704306
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GnomAD4 genome AF: 0.000203 AC: 31AN: 152376Hom.: 1 Cov.: 34 AF XY: 0.000201 AC XY: 15AN XY: 74516
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.505A>G (p.I169V) alteration is located in exon 4 (coding exon 3) of the TRPV2 gene. This alteration results from a A to G substitution at nucleotide position 505, causing the isoleucine (I) at amino acid position 169 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at