Variant rs7621642 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001251845.2(TRPC1):c.1020G>A(p.Ser340Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 1,613,628 control chromosomes in the GnomAD database, including 55,615 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 0.35 ( 12693 hom., cov: 33)

Exomes 𝑓: 0.23 ( 42922 hom. )

Consequence

TRPC1
NM_001251845.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0190

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:

TRPC1 (HGNC:):

TRPC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP7

Synonymous conserved (PhyloP=-0.019 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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.1020G>A	p.Ser340Ser	synonymous_variant	7/13	ENST00000476941.6	NP_001238774.1	P48995-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRPC1	ENST00000476941.6 linkuse as main transcript	c.1020G>A	p.Ser340Ser	synonymous_variant	7/13	1	NM_001251845.2	ENSP00000419313.1	P48995-1
TRPC1	ENST00000273482.10 linkuse as main transcript	c.918G>A	p.Ser306Ser	synonymous_variant	6/12	1		ENSP00000273482.6	P48995-2
TRPC1	ENST00000698238.1 linkuse as main transcript	c.1329G>A	p.Ser443Ser	synonymous_variant	7/13			ENSP00000513620.1	A0A8V8TLK5
TRPC1	ENST00000480101.1 linkuse as main transcript	n.150G>A		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52818

AN:

151906

Hom.:

12642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.689

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.295

GnomAD3 exomes

AF:

0.246

AC:

61861

AN:

251134

Hom.:

10060

AF XY:

0.236

AC XY:

32004

AN XY:

135718

show subpopulations

Gnomad AFR exome

AF:

0.699

Gnomad AMR exome

AF:

0.184

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.412

Gnomad SAS exome

AF:

0.205

Gnomad FIN exome

AF:

0.203

Gnomad NFE exome

AF:

0.207

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.227

AC:

331665

AN:

1461604

Hom.:

42922

Cov.:

AF XY:

0.223

AC XY:

162488

AN XY:

727096

show subpopulations

Gnomad4 AFR exome

AF:

0.711

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.121

Gnomad4 EAS exome

AF:

0.376

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.202

Gnomad4 NFE exome

AF:

0.213

Gnomad4 OTH exome

AF:

0.248

GnomAD4 genome

AF:

0.348

AC:

52927

AN:

152024

Hom.:

12693

Cov.:

AF XY:

0.343

AC XY:

25489

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.690

Gnomad4 AMR

AF:

0.215

Gnomad4 ASJ

AF:

0.125

Gnomad4 EAS

AF:

0.432

Gnomad4 SAS

AF:

0.211

Gnomad4 FIN

AF:

0.202

Gnomad4 NFE

AF:

0.212

Gnomad4 OTH

AF:

0.303

Alfa

AF:

0.227

Hom.:

10723

Bravo

AF:

0.365

Asia WGS

AF:

0.348

AC:

1211

AN:

3478

EpiCase

AF:

0.209

EpiControl

AF:

0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

9.4

DANN

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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