rs733080

Variant names:

• chr17-3597317-T-C
• rs733080
• NM_080704.4:c.-33-4934A>G

Variant summary

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

The NM_080704.4(TRPV1):​c.-33-4934A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,118 control chromosomes in the GnomAD database, including 15,411 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 0.40 (15411 hom., cov: 32)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 1 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 = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPV1	NM_080704.4	c.-33-4934A>G		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.-33-4934A>G		intron_variant	Intron 2 of 16	1	NM_080704.4	ENSP00000459962.1
ENSG00000262304	ENST00000572919.1	n.*1252-4934A>G		intron_variant	Intron 7 of 13	5		ENSP00000461416.1
TRPV1	ENST00000571088.5	c.-433A>G		upstream_gene_variant		1		ENSP00000461007.1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60399 AN: 152000 Hom.: 15374 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.398 AC: 60487 AN: 152118 Hom.: 15411 Cov.: 32 AF XY: 0.390 AC XY: 29039 AN XY: 74370

African (AFR) AF: 0.732 AC: 30358 AN: 41488

American (AMR) AF: 0.340 AC: 5196 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3466

East Asian (EAS) AF: 0.189 AC: 976 AN: 5172

South Asian (SAS) AF: 0.291 AC: 1404 AN: 4826

European-Finnish (FIN) AF: 0.223 AC: 2359 AN: 10588

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18165 AN: 67966

Other (OTH) AF: 0.376 AC: 795 AN: 2114

Alfa AF: 0.349 Hom.: 1890

Bravo AF: 0.420

Asia WGS AF: 0.240 AC: 834 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	9.3
DANN	Benign	0.73
PhyloP100		0.33
PromoterAI		-0.018	Neutral

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: rs733080; hg19: chr17-3500611;