rs17707155

chr17-3601939-C-T

Variant summary

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

The NM_080704.4(TRPV1):c.-34+6488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,074 control chromosomes in the GnomAD database, including 3,869 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 0.20 (3869 hom., cov: 31)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPV1	NM_080704.4	c.-34+6488G>A		intron_variant		ENST00000572705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPV1	ENST00000572705.2	c.-34+6488G>A		intron_variant		1	NM_080704.4	P1
	ENST00000575593.1	n.334G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30882 AN: 151936 Hom.: 3867 Cov.: 31

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.300 AC: 6 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.357 AC XY: 5 AN XY: 14

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.203 AC: 30893 AN: 152054 Hom.: 3869 Cov.: 31 AF XY: 0.202 AC XY: 14984 AN XY: 74308

Gnomad4 AFR AF: 0.0950

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.223

Alfa AF: 0.253 Hom.: 6620

Bravo AF: 0.192

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.22
Dann	Benign	0.65

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: rs17707155; hg19: chr17-3505233;