3-142784763-G-T

Variant names:

• chr3-142784763-G-T
• rs7621642
• NM_001251845.2:c.1020G>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001251845.2(TRPC1):​c.1020G>T​(p.Ser340Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: TRPC1 NM_001251845.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 23 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BP7: Synonymous conserved (PhyloP=-0.019 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001251845.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPC1	NM_001251845.2	MANE Select	c.1020G>T	p.Ser340Ser	synonymous	Exon 7 of 13	NP_001238774.1
	TRPC1	NM_003304.5		c.918G>T	p.Ser306Ser	synonymous	Exon 6 of 12	NP_003295.1
	TRPC1	NM_001413361.1		c.870G>T	p.Ser290Ser	synonymous	Exon 6 of 12	NP_001400290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPC1	ENST00000476941.6	TSL:1 MANE Select	c.1020G>T	p.Ser340Ser	synonymous	Exon 7 of 13	ENSP00000419313.1
	TRPC1	ENST00000273482.10	TSL:1	c.918G>T	p.Ser306Ser	synonymous	Exon 6 of 12	ENSP00000273482.6
	TRPC1	ENST00000698238.1		c.1329G>T	p.Ser443Ser	synonymous	Exon 7 of 13	ENSP00000513620.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	5.5
DANN	Benign	0.73
PhyloP100		-0.019
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

Other links and lift over

dbSNP: rs7621642; hg19: chr3-142503605;