17-3596076-G-C

Position:

• chr17-3596076-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080704.4(TRPV1):​c.-33-3693C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,166 control chromosomes in the GnomAD database, including 6,278 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 0.16 (6278 hom., cov: 32)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPV1	NM_080704.4	c.-33-3693C>G		intron_variant		ENST00000572705.2
TRPV1	NM_018727.5	c.-34+842C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPV1	ENST00000572705.2	c.-33-3693C>G		intron_variant		1	NM_080704.4	P1
TRPV1	ENST00000571088.5	c.-34+842C>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24173 AN: 152046 Hom.: 6259 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00268

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.159 AC: 24238 AN: 152166 Hom.: 6278 Cov.: 32 AF XY: 0.154 AC XY: 11489 AN XY: 74428

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0233

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.00266

Gnomad4 OTH AF: 0.114

Alfa AF: 0.00612 Hom.: 21

Bravo AF: 0.184

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.71

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: rs10491214; hg19: chr17-3499370;