Variant 3-142806016-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001251845.2(TRPC1):c.2163G>A(p.Arg721=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,611,862 control chromosomes in the GnomAD database, including 46,493 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 0.32 ( 11232 hom., cov: 32)

Exomes 𝑓: 0.20 ( 35261 hom. )

Consequence

TRPC1
NM_001251845.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.65

Variant links:

Genes affected

TRPC1 (HGNC:12333): (transient receptor potential cation channel subfamily C member 1) The protein encoded by this gene is a membrane protein that can form a non-selective channel permeable to calcium and other cations. The encoded protein appears to be induced to form channels by a receptor tyrosine kinase-activated phosphatidylinositol second messenger system and also by depletion of intracellular calcium stores. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

TRPC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP7

Synonymous conserved (PhyloP=2.65 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPC1	NM_001251845.2 linkuse as main transcript	c.2163G>A	p.Arg721=	synonymous_variant	13/13	ENST00000476941.6	NP_001238774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPC1	ENST00000476941.6 linkuse as main transcript	c.2163G>A	p.Arg721=	synonymous_variant	13/13	1	NM_001251845.2	ENSP00000419313	P1	P48995-1
TRPC1	ENST00000273482.10 linkuse as main transcript	c.2061G>A	p.Arg687=	synonymous_variant	12/12	1		ENSP00000273482		P48995-2
TRPC1	ENST00000698238.1 linkuse as main transcript	c.2472G>A	p.Arg824=	synonymous_variant	13/13			ENSP00000513620

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48963

AN:

151856

Hom.:

11194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.658

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.367

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.276

GnomAD3 exomes

AF:

0.222

AC:

55598

AN:

250202

Hom.:

8365

AF XY:

0.211

AC XY:

28568

AN XY:

135192

show subpopulations

Gnomad AFR exome

AF:

0.666

Gnomad AMR exome

AF:

0.175

Gnomad ASJ exome

AF:

0.113

Gnomad EAS exome

AF:

0.355

Gnomad SAS exome

AF:

0.172

Gnomad FIN exome

AF:

0.179

Gnomad NFE exome

AF:

0.184

Gnomad OTH exome

AF:

0.191

GnomAD4 exome

AF:

0.204

AC:

298177

AN:

1459888

Hom.:

35261

Cov.:

AF XY:

0.200

AC XY:

145508

AN XY:

726122

show subpopulations

Gnomad4 AFR exome

AF:

0.679

Gnomad4 AMR exome

AF:

0.182

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.313

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.178

Gnomad4 NFE exome

AF:

0.192

Gnomad4 OTH exome

AF:

0.226

GnomAD4 genome

AF:

0.323

AC:

49055

AN:

151974

Hom.:

11232

Cov.:

AF XY:

0.318

AC XY:

23589

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.658

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.367

Gnomad4 SAS

AF:

0.181

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.189

Gnomad4 OTH

AF:

0.284

Alfa

AF:

0.219

Hom.:

3823

Bravo

AF:

0.341

Asia WGS

AF:

0.316

AC:

1100

AN:

3478

EpiCase

AF:

0.187

EpiControl

AF:

0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

5.6

DANN

Benign

0.81

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