rs3826503

Variant names:

• chr17-3571366-G-A
• rs3826503
• NM_080704.4:c.2347+158C>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.2347+158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,174 control chromosomes in the GnomAD database, including 2,874 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 0.18 (2874 hom., cov: 33)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080704.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPV1	NM_080704.4	MANE Select	c.2347+158C>T		intron	N/A	NP_542435.2	Q8NER1-1
	TRPV1	NM_018727.5		c.2347+158C>T		intron	N/A	NP_061197.4	Q8NER1-1
	TRPV1	NM_080705.4		c.2347+158C>T		intron	N/A	NP_542436.2	Q8NER1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPV1	ENST00000572705.2	TSL:1 MANE Select	c.2347+158C>T		intron	N/A	ENSP00000459962.1	Q8NER1-1
	TRPV1	ENST00000425167.6	TSL:1	c.2380+158C>T		intron	N/A	ENSP00000409627.2	E7EQ78
	TRPV1	ENST00000399756.8	TSL:1	c.2347+158C>T		intron	N/A	ENSP00000382659.4	Q8NER1-1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26740 AN: 152054 Hom.: 2873 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.176 AC: 26765 AN: 152174 Hom.: 2874 Cov.: 33 AF XY: 0.184 AC XY: 13660 AN XY: 74368

African (AFR) AF: 0.108 AC: 4482 AN: 41544

American (AMR) AF: 0.204 AC: 3115 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2735 AN: 5138

South Asian (SAS) AF: 0.196 AC: 949 AN: 4830

European-Finnish (FIN) AF: 0.251 AC: 2660 AN: 10604

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11372 AN: 67986

Other (OTH) AF: 0.193 AC: 407 AN: 2114

Alfa AF: 0.170 Hom.: 2712

Bravo AF: 0.175

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.68
PhyloP100		-1.1
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: rs3826503; hg19: chr17-3474660;