chr3-142784761-TCG-AGC

Variant names:

• chr3-142784761-TCG-AGC
• NM_001251845.2:c.1018_1020delTCGinsAGC
• TRPC1 p.341

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_001251845.2(TRPC1):​c.1018_1020delTCGinsAGC​(p.341) variant causes a synonymous change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. 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: 7.53
• Publications: 0 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: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPC1	NM_001251845.2	MANE Select	c.1018_1020delTCGinsAGC	p.341	synonymous	N/A	NP_001238774.1	P48995-1
	TRPC1	NM_003304.5		c.916_918delTCGinsAGC	p.307	synonymous	N/A	NP_003295.1	P48995-2
	TRPC1	NM_001413361.1		c.868_870delTCGinsAGC	p.291	synonymous	N/A	NP_001400290.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPC1	ENST00000476941.6	TSL:1 MANE Select	c.1018_1020delTCGinsAGC	p.341	synonymous	N/A	ENSP00000419313.1	P48995-1
	TRPC1	ENST00000273482.10	TSL:1	c.916_918delTCGinsAGC	p.307	synonymous	N/A	ENSP00000273482.6	P48995-2
	TRPC1	ENST00000698238.1		c.1327_1329delTCGinsAGC	p.444	synonymous	N/A	ENSP00000513620.1	A0A8V8TLK5

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr3-142503603;