17-3600233-T-G

Variant names:

• chr17-3600233-T-G
• rs161381
• NM_080704.4:c.-33-7850A>C

Variant summary

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

The NM_080704.4(TRPV1):​c.-33-7850A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,146 control chromosomes in the GnomAD database, including 55,626 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 0.85 (55626 hom., cov: 31)
• Consequence: TRPV1 NM_080704.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 6 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPV1	NM_080704.4	c.-33-7850A>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.-33-7850A>C		intron_variant	Intron 2 of 16	1	NM_080704.4	ENSP00000459962.1
ENSG00000262304	ENST00000572919.1	n.*1252-7850A>C		intron_variant	Intron 7 of 13	5		ENSP00000461416.1

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129724 AN: 152028 Hom.: 55576 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.853 AC: 129829 AN: 152146 Hom.: 55626 Cov.: 31 AF XY: 0.854 AC XY: 63540 AN XY: 74372

African (AFR) AF: 0.884 AC: 36688 AN: 41498

American (AMR) AF: 0.853 AC: 13029 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2871 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5167 AN: 5180

South Asian (SAS) AF: 0.800 AC: 3860 AN: 4826

European-Finnish (FIN) AF: 0.863 AC: 9128 AN: 10582

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56191 AN: 68000

Other (OTH) AF: 0.868 AC: 1833 AN: 2112

Alfa AF: 0.821 Hom.: 22421

Bravo AF: 0.857

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.62
PhyloP100		-1.4

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: rs161381; hg19: chr17-3503527;