rs2074891314

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_080704.4(TRPV1):​c.2017A>G​(p.Ile673Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

TRPV1
NM_080704.4 missense

Scores

10
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.78
Variant links:
Genes affected
TRPV1 (HGNC:12716): (transient receptor potential cation channel subfamily V member 1) Capsaicin, the main pungent ingredient in hot chili peppers, elicits a sensation of burning pain by selectively activating sensory neurons that convey information about noxious stimuli to the central nervous system. The protein encoded by this gene is a receptor for capsaicin and is a non-selective cation channel that is structurally related to members of the TRP family of ion channels. This receptor is also activated by increases in temperature in the noxious range, suggesting that it functions as a transducer of painful thermal stimuli in vivo. Four transcript variants encoding the same protein, but with different 5' UTR sequence, have been described for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.27720985).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRPV1NM_080704.4 linkc.2017A>G p.Ile673Val missense_variant Exon 14 of 17 ENST00000572705.2 NP_542435.2 Q8NER1-1
TRPV1NM_018727.5 linkc.2017A>G p.Ile673Val missense_variant Exon 13 of 16 NP_061197.4 Q8NER1-1
TRPV1NM_080705.4 linkc.2017A>G p.Ile673Val missense_variant Exon 13 of 16 NP_542436.2 Q8NER1-1
TRPV1NM_080706.3 linkc.2017A>G p.Ile673Val missense_variant Exon 12 of 15 NP_542437.2 Q8NER1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRPV1ENST00000572705.2 linkc.2017A>G p.Ile673Val missense_variant Exon 14 of 17 1 NM_080704.4 ENSP00000459962.1 Q8NER1-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461862
Hom.:
0
Cov.:
34
AF XY:
0.00
AC XY:
0
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Uncertain
-0.050
CADD
Benign
23
DANN
Benign
0.97
DEOGEN2
Uncertain
0.63
D;D;D;D;.;.;.
Eigen
Benign
0.14
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.87
.;.;.;D;D;D;T
M_CAP
Benign
0.061
D
MetaRNN
Benign
0.28
T;T;T;T;T;T;T
MetaSVM
Uncertain
-0.20
T
MutationAssessor
Benign
1.1
L;L;L;L;.;.;.
PrimateAI
Uncertain
0.74
T
PROVEAN
Benign
-0.38
N;.;.;N;N;.;N
REVEL
Uncertain
0.46
Sift
Benign
0.60
T;.;.;T;T;.;T
Sift4G
Benign
0.74
T;T;T;T;T;T;T
Polyphen
0.17
B;B;B;B;P;.;B
Vest4
0.44
MutPred
0.41
.;.;.;.;Gain of catalytic residue at I684 (P = 0.0893);.;.;
MVP
0.46
MPC
0.067
ClinPred
0.46
T
GERP RS
5.6
Varity_R
0.12
gMVP
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-3477013; API