rs182637

Positions:

• chr17-3606538-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000572705.2(TRPV1):​c.-34+1889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,046 control chromosomes in the GnomAD database, including 12,951 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: 𝑓 0.38 (12951 hom., cov: 32)
• Consequence: TRPV1 ENST00000572705.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPV1	NM_080704.4	c.-34+1889G>A		intron_variant		ENST00000572705.2	NP_542435.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPV1	ENST00000572705.2	c.-34+1889G>A		intron_variant		1	NM_080704.4	ENSP00000459962	P1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58149 AN: 151928 Hom.: 12953 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.430

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.382 AC: 58133 AN: 152046 Hom.: 12951 Cov.: 32 AF XY: 0.388 AC XY: 28843 AN XY: 74308

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.427

Alfa AF: 0.417 Hom.: 5229

Bravo AF: 0.372

Asia WGS AF: 0.500 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.72

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: rs182637; hg19: chr17-3509832;