rs161364

Variant names:

• chr17-3574518-C-T
• rs161364
• NM_080704.4:c.1781-563G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080704.4(TRPV1):​c.1781-563G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,206 control chromosomes in the GnomAD database, including 4,937 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 0.23 (4937 hom., cov: 31)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPV1	NM_080704.4	c.1781-563G>A		intron_variant	Intron 13 of 16	ENST00000572705.2	NP_542435.2
TRPV1	NM_018727.5	c.1781-563G>A		intron_variant	Intron 12 of 15		NP_061197.4
TRPV1	NM_080705.4	c.1781-563G>A		intron_variant	Intron 12 of 15		NP_542436.2
TRPV1	NM_080706.3	c.1781-563G>A		intron_variant	Intron 11 of 14		NP_542437.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPV1	ENST00000572705.2	c.1781-563G>A		intron_variant	Intron 13 of 16	1	NM_080704.4	ENSP00000459962.1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34801 AN: 152088 Hom.: 4936 Cov.: 31

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.229 AC: 34813 AN: 152206 Hom.: 4937 Cov.: 31 AF XY: 0.231 AC XY: 17187 AN XY: 74412

African (AFR) AF: 0.0560 AC: 2328 AN: 41550

American (AMR) AF: 0.300 AC: 4578 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1311 AN: 5176

South Asian (SAS) AF: 0.371 AC: 1791 AN: 4824

European-Finnish (FIN) AF: 0.286 AC: 3027 AN: 10592

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19979 AN: 68004

Other (OTH) AF: 0.248 AC: 524 AN: 2110

Alfa AF: 0.285 Hom.: 3667

Bravo AF: 0.219

Asia WGS AF: 0.311 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.55
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs161364; hg19: chr17-3477812;