rs201778834

Variant names:

• chr17-3566927-C-G
• rs201778834
• NM_080704.4:c.2408G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-3566927-C-G
• chr17-3566927-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_080704.4(TRPV1):​c.2408G>C​(p.Arg803Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TRPV1 NM_080704.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.75

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPV1	NM_080704.4	c.2408G>C	p.Arg803Pro	missense_variant	Exon 17 of 17	ENST00000572705.2	NP_542435.2
TRPV1	NM_018727.5	c.2408G>C	p.Arg803Pro	missense_variant	Exon 16 of 16		NP_061197.4
TRPV1	NM_080705.4	c.2408G>C	p.Arg803Pro	missense_variant	Exon 16 of 16		NP_542436.2
TRPV1	NM_080706.3	c.2408G>C	p.Arg803Pro	missense_variant	Exon 15 of 15		NP_542437.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPV1	ENST00000572705.2	c.2408G>C	p.Arg803Pro	missense_variant	Exon 17 of 17	1	NM_080704.4	ENSP00000459962.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.40	T;T;T;T;.;.;.
Eigen	Uncertain	0.35
Eigen_PC	Uncertain	0.36
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.80	.;.;.;T;T;T;T
M_CAP	Benign	0.070	D
MetaRNN	Uncertain	0.59	D;D;D;D;D;D;D
MetaSVM	Uncertain	0.67	D
MutationAssessor	Uncertain	2.2	M;M;M;M;.;.;.
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-1.6	N;.;.;N;N;.;N
REVEL	Uncertain	0.54
Sift	Uncertain	0.0080	D;.;.;D;D;.;D
Sift4G	Uncertain	0.053	T;T;T;T;T;T;T
Polyphen		0.029	B;B;B;B;D;.;D
Vest4		0.50
MutPred		0.23		.;.;.;.;Loss of solvent accessibility (P = 0.0199);.;.;
MVP		0.67
MPC		0.095
ClinPred		0.94	D
GERP RS		5.5
Varity_R		0.61
gMVP		0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs201778834; hg19: chr17-3470221;