Variant chr4-121902897-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001130698.2(TRPC3):c.2418G>A(p.Arg806Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,612,158 control chromosomes in the GnomAD database, including 96,867 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 6925 hom., cov: 32)

Exomes 𝑓: 0.35 ( 89942 hom. )

Consequence

TRPC3
NM_001130698.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.635

Variant links:

Genes affected

TRPC3 (HGNC:12335): (transient receptor potential cation channel subfamily C member 3) 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]

TRPC3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 4-121902897-C-T is Benign according to our data. Variant chr4-121902897-C-T is described in ClinVar as [Benign]. Clinvar id is 2135323.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.635 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPC3	NM_001130698.2 linkuse as main transcript	c.2418G>A	p.Arg806Arg	synonymous_variant	9/12	ENST00000379645.8	NP_001124170.1	Q13507-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPC3	ENST00000379645.8 linkuse as main transcript	c.2418G>A	p.Arg806Arg	synonymous_variant	9/12	1	NM_001130698.2	ENSP00000368966.3		Q13507-2

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43436

AN:

151846

Hom.:

6920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.343

AC:

85799

AN:

250284

Hom.:

15513

AF XY:

0.341

AC XY:

46068

AN XY:

135274

show subpopulations

Gnomad AFR exome

AF:

0.123

Gnomad AMR exome

AF:

0.454

Gnomad ASJ exome

AF:

0.288

Gnomad EAS exome

AF:

0.413

Gnomad SAS exome

AF:

0.320

Gnomad FIN exome

AF:

0.377

Gnomad NFE exome

AF:

0.333

Gnomad OTH exome

AF:

0.346

GnomAD4 exome

AF:

0.347

AC:

506179

AN:

1460194

Hom.:

89942

Cov.:

AF XY:

0.345

AC XY:

250400

AN XY:

726356

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.442

Gnomad4 ASJ exome

AF:

0.281

Gnomad4 EAS exome

AF:

0.488

Gnomad4 SAS exome

AF:

0.325

Gnomad4 FIN exome

AF:

0.390

Gnomad4 NFE exome

AF:

0.347

Gnomad4 OTH exome

AF:

0.331

GnomAD4 genome

AF:

0.286

AC:

43455

AN:

151964

Hom.:

6925

Cov.:

AF XY:

0.291

AC XY:

21629

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.133

Gnomad4 AMR

AF:

0.368

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.427

Gnomad4 SAS

AF:

0.327

Gnomad4 FIN

AF:

0.374

Gnomad4 NFE

AF:

0.333

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.318

Hom.:

9378

Bravo

AF:

0.278

Asia WGS

AF:

0.346

AC:

1204

AN:

3478

EpiCase

AF:

0.319

EpiControl

AF:

0.324

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over