chr17-3601032-A-G

Variant names:

• chr17-3601032-A-G
• rs161380
• NM_080704.4:c.-34+7395T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_080704.4(TRPV1):​c.-34+7395T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 151,712 control chromosomes in the GnomAD database, including 52,882 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.83 (52882 hom., cov: 28)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.352
• Publications: 0 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 17-3601032-A-G is Benign according to our data. Variant chr17-3601032-A-G is described in ClinVar as [Benign]. Clinvar id is 189125.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPV1	NM_080704.4	c.-34+7395T>C		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+7395T>C		intron_variant	Intron 2 of 16	1	NM_080704.4	ENSP00000459962.1
ENSG00000262304	ENST00000572919.1	n.*1251+8277T>C		intron_variant	Intron 7 of 13	5		ENSP00000461416.1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126341 AN: 151594 Hom.: 52848 Cov.: 28

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.833 AC: 126426 AN: 151712 Hom.: 52882 Cov.: 28 AF XY: 0.835 AC XY: 61903 AN XY: 74114

African (AFR) AF: 0.808 AC: 33384 AN: 41324

American (AMR) AF: 0.848 AC: 12921 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2885 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5104 AN: 5118

South Asian (SAS) AF: 0.810 AC: 3882 AN: 4794

European-Finnish (FIN) AF: 0.864 AC: 9134 AN: 10576

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56254 AN: 67876

Other (OTH) AF: 0.857 AC: 1807 AN: 2108

Alfa AF: 0.797 Hom.: 3541

Bravo AF: 0.835

Asia WGS AF: 0.903 AC: 3141 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Nephropathic cystinosis Benign:1

Jan 14, 2015

Counsyl

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.30
DANN	Benign	0.29
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: rs161380; hg19: chr17-3504326;