dbSNP rs879114: TRPC2:n.1125-94G>A (chr11-3622548-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000451043.8(TRPC2):n.1125-94G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,470 control chromosomes in the GnomAD database, including 3,008 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 0.19 ( 3004 hom., cov: 31)

Exomes 𝑓: 0.13 ( 4 hom. )

Consequence

TRPC2
ENST00000451043.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0210

Publications

3 publications found

Variant links:

Genes affected

TRPC2 (HGNC:12334): (transient receptor potential cation channel subfamily C member 2 (pseudogene)) Predicted to enable several functions, including calmodulin binding activity; diacylglycerol binding activity; and inositol 1,4,5 trisphosphate binding activity. Predicted to act upstream of or within several processes, including inter-male aggressive behavior; mating behavior; and territorial aggressive behavior. Predicted to be located in several cellular components, including Golgi membrane; dendrite membrane; and nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

TRPC2 links:

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new If you want to explore the variant's impact on the transcript ENST00000451043.8, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451043.8. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPC2	ENST00000451043.8		n.1125-94G>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29380

AN:

151872

Hom.:

3000

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.225

GnomAD4 exome

AF:

0.126

AC:

AN:

478

Hom.:

AF XY:

0.0903

AC XY:

AN XY:

288

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.128

AC:

AN:

436

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0938

AC:

AN:

Other (OTH)

AF:

0.125

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.193

AC:

29406

AN:

151992

Hom.:

3004

Cov.:

AF XY:

0.194

AC XY:

14383

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.243

AC:

10067

AN:

41426

American (AMR)

AF:

0.178

AC:

2723

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.272

AC:

944

AN:

3466

East Asian (EAS)

AF:

0.161

AC:

830

AN:

5170

South Asian (SAS)

AF:

0.252

AC:

1211

AN:

4800

European-Finnish (FIN)

AF:

0.117

AC:

1241

AN:

10580

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.172

AC:

11668

AN:

67966

Other (OTH)

AF:

0.227

AC:

478

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1202

2405

3607

4810

6012

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

322

644

966

1288

1610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.187

Hom.:

12488

Bravo

AF:

0.199

Asia WGS

AF:

0.208

AC:

723

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.8

(source)

DANN

Benign

0.71

PhyloP100

-0.021

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over