rs222741

Variant names:

• chr17-3605586-G-A
• rs222741
• NM_080704.4:c.-34+2841C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-3605586-G-A
• chr17-3605586-G-C
• chr17-3605586-G-T

Variant summary

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

The NM_080704.4(TRPV1):​c.-34+2841C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,940 control chromosomes in the GnomAD database, including 45,171 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 0.77 (45171 hom., cov: 31)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 24 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]

ENSG00000262304 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPV1	NM_080704.4	c.-34+2841C>T		intron_variant	Intron 2 of 16	ENST00000572705.2	NP_542435.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPV1	ENST00000572705.2	c.-34+2841C>T		intron_variant	Intron 2 of 16	1	NM_080704.4	ENSP00000459962.1
ENSG00000262304	ENST00000572919.1	n.*1251+3723C>T		intron_variant	Intron 7 of 13	5		ENSP00000461416.1

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116543 AN: 151822 Hom.: 45145 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.767 AC: 116614 AN: 151940 Hom.: 45171 Cov.: 31 AF XY: 0.766 AC XY: 56917 AN XY: 74270

African (AFR) AF: 0.861 AC: 35706 AN: 41448

American (AMR) AF: 0.749 AC: 11425 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2565 AN: 3472

East Asian (EAS) AF: 0.770 AC: 3979 AN: 5168

South Asian (SAS) AF: 0.615 AC: 2958 AN: 4806

European-Finnish (FIN) AF: 0.787 AC: 8300 AN: 10542

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49128 AN: 67938

Other (OTH) AF: 0.778 AC: 1641 AN: 2108

Alfa AF: 0.736 Hom.: 108845

Bravo AF: 0.774

Asia WGS AF: 0.630 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.35

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: rs222741; hg19: chr17-3508880;