Variant 17-3591067-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_080704.4(TRPV1):c.501C>T(p.His167His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,612,620 control chromosomes in the GnomAD database, including 13,651 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.10 ( 1000 hom., cov: 32)

Exomes 𝑓: 0.12 ( 12651 hom. )

Consequence

TRPV1
NM_080704.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.727

Variant links:

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]

TRPV1 links:

ENSG00000262304 (HGNC:):

ENSG00000262304 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 17-3591067-G-A is Benign according to our data. Variant chr17-3591067-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.727 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPV1	NM_080704.4 linkuse as main transcript	c.501C>T	p.His167His	synonymous_variant	5/17	ENST00000572705.2	NP_542435.2	Q8NER1-1
TRPV1	NM_018727.5 linkuse as main transcript	c.501C>T	p.His167His	synonymous_variant	4/16		NP_061197.4	Q8NER1-1
TRPV1	NM_080705.4 linkuse as main transcript	c.501C>T	p.His167His	synonymous_variant	4/16		NP_542436.2	Q8NER1-1
TRPV1	NM_080706.3 linkuse as main transcript	c.501C>T	p.His167His	synonymous_variant	3/15		NP_542437.2	Q8NER1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRPV1	ENST00000572705.2 linkuse as main transcript	c.501C>T	p.His167His	synonymous_variant	5/17	1	NM_080704.4	ENSP00000459962.1	Q8NER1-1
ENSG00000262304	ENST00000572919.1 linkuse as main transcript	n.*1785C>T		non_coding_transcript_exon_variant	10/14	5		ENSP00000461416.1	A0A0B4J2A0
ENSG00000262304	ENST00000572919.1 linkuse as main transcript	n.*1785C>T		3_prime_UTR_variant	10/14	5		ENSP00000461416.1	A0A0B4J2A0

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15792

AN:

152088

Hom.:

998

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0415

Gnomad AMI

AF:

0.0493

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.107

GnomAD3 exomes

AF:

0.136

AC:

33621

AN:

246538

Hom.:

2678

AF XY:

0.139

AC XY:

18653

AN XY:

133750

show subpopulations

Gnomad AFR exome

AF:

0.0365

Gnomad AMR exome

AF:

0.142

Gnomad ASJ exome

AF:

0.122

Gnomad EAS exome

AF:

0.241

Gnomad SAS exome

AF:

0.230

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.111

Gnomad OTH exome

AF:

0.117

GnomAD4 exome

AF:

0.125

AC:

181881

AN:

1460414

Hom.:

12651

Cov.:

AF XY:

0.127

AC XY:

92205

AN XY:

726360

show subpopulations

Gnomad4 AFR exome

AF:

0.0368

Gnomad4 AMR exome

AF:

0.141

Gnomad4 ASJ exome

AF:

0.122

Gnomad4 EAS exome

AF:

0.265

Gnomad4 SAS exome

AF:

0.222

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.114

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.104

AC:

15802

AN:

152206

Hom.:

1000

Cov.:

AF XY:

0.107

AC XY:

7993

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0415

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.238

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.113

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.106

Hom.:

796

Bravo

AF:

0.0984

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.6

DANN

Benign

0.53

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over