17-3601032-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate 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 (★).

• Frequency: Genomes: 𝑓 0.83 (52882 hom., cov: 28)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.352

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

Verdict is Benign. Variant got -14 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 criteria_provided_single_submitter, 1 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/exons	MANE	UniProt
TRPV1	NM_080704.4	c.-34+7395T>C		intron_variant		ENST00000572705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPV1	ENST00000572705.2	c.-34+7395T>C		intron_variant		1	NM_080704.4	P1

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

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.857

Alfa AF: 0.795 Hom.: 3279

Bravo AF: 0.835

Asia WGS AF: 0.903 AC: 3141 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Nephropathic cystinosis Benign:1

Benign, criteria provided, single submitter

literature only

Counsyl

Jan 14, 2015

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.30
Dann	Benign	0.29

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

Publications

LitVar

Other links and lift over

dbSNP: rs161380; hg19: chr17-3504326;