Variant rs196432 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412742.5(RCAN3):c.491G>A(p.Arg164Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,588,326 control chromosomes in the GnomAD database, including 182,348 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 16764 hom., cov: 33)

Exomes 𝑓: 0.48 ( 165584 hom. )

Consequence

RCAN3
ENST00000412742.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.51

Variant links:

Genes affected

RCAN3 (HGNC:3042): (RCAN family member 3) Enables phosphatase binding activity and troponin I binding activity. Predicted to be involved in calcium-mediated signaling. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

RCAN3 links:

RCAN3AS (HGNC:39009): (RCAN3 antisense RNA)

RCAN3AS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.77613E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RCAN3	NM_013441.4 linkuse as main transcript	c.663G>A	p.Thr221=	synonymous_variant	5/5	ENST00000374395.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RCAN3	ENST00000374395.9 linkuse as main transcript	c.663G>A	p.Thr221=	synonymous_variant	5/5	1	NM_013441.4	P1	Q9UKA8-1
RCAN3AS	ENST00000651630.1 linkuse as main transcript	n.142+45C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70702

AN:

151946

Hom.:

16755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.460

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.725

Gnomad SAS

AF:

0.477

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.415

GnomAD3 exomes

AF:

0.472

AC:

106249

AN:

225008

Hom.:

25790

AF XY:

0.472

AC XY:

58052

AN XY:

123048

show subpopulations

Gnomad AFR exome

AF:

0.462

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.379

Gnomad EAS exome

AF:

0.708

Gnomad SAS exome

AF:

0.469

Gnomad FIN exome

AF:

0.495

Gnomad NFE exome

AF:

0.471

Gnomad OTH exome

AF:

0.442

GnomAD4 exome

AF:

0.477

AC:

684694

AN:

1436262

Hom.:

165584

Cov.:

AF XY:

0.475

AC XY:

339842

AN XY:

714754

show subpopulations

Gnomad4 AFR exome

AF:

0.456

Gnomad4 AMR exome

AF:

0.381

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.737

Gnomad4 SAS exome

AF:

0.467

Gnomad4 FIN exome

AF:

0.498

Gnomad4 NFE exome

AF:

0.474

Gnomad4 OTH exome

AF:

0.476

GnomAD4 genome

AF:

0.465

AC:

70735

AN:

152064

Hom.:

16764

Cov.:

AF XY:

0.464

AC XY:

34510

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.459

Gnomad4 AMR

AF:

0.387

Gnomad4 ASJ

AF:

0.401

Gnomad4 EAS

AF:

0.726

Gnomad4 SAS

AF:

0.479

Gnomad4 FIN

AF:

0.493

Gnomad4 NFE

AF:

0.467

Gnomad4 OTH

AF:

0.421

Alfa

AF:

0.461

Hom.:

39076

Bravo

AF:

0.459

TwinsUK

AF:

0.475

AC:

1761

ALSPAC

AF:

0.473

AC:

1822

ESP6500AA

AF:

0.464

AC:

2045

ESP6500EA

AF:

0.461

AC:

3966

ExAC

AF:

0.481

AC:

58383

Asia WGS

AF:

0.642

AC:

2231

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

0.068

DANN

Benign

0.87

Eigen

Benign

-2.2

Eigen_PC

Benign

-2.3

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.55

T;T

MetaRNN

Benign

9.8e-7

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

P;P;P;P;P

PROVEAN

Benign

0.68

N;N

REVEL

Benign

0.039

Sift

Benign

1.0

T;T

Sift4G

Benign

0.84

T;T

Vest4

0.10

ClinPred

0.013

GERP RS

-12

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