Genetic Variant CAMTA2:p.Ala267Pro (chr17-4980523-C-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015099.4(CAMTA2):c.799G>C(p.Ala267Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 1,600,024 control chromosomes in the GnomAD database, including 502,365 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.82 ( 48756 hom., cov: 19)

Exomes 𝑓: 0.78 ( 453609 hom. )

Consequence

CAMTA2
NM_015099.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.379

Variant links:

Genes affected

CAMTA2 (HGNC:18807): (calmodulin binding transcription activator 2) The protein encoded by this gene is a member of the calmodulin-binding transcription activator protein family. Members of this family share a common domain structure that consists of a transcription activation domain, a DNA-binding domain, and a calmodulin-binding domain. The encoded protein may be a transcriptional coactivator of genes involved in cardiac growth. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jan 2010]

CAMTA2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.3856694E-7).

BP6

Variant 17-4980523-C-G is Benign according to our data. Variant chr17-4980523-C-G is described in ClinVar as [Benign]. Clinvar id is 1270598.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMTA2	NM_015099.4 link	c.799G>C	p.Ala267Pro	missense_variant	Exon 9 of 23	ENST00000348066.8	NP_055914.2	O94983-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMTA2	ENST00000348066.8 link	c.799G>C	p.Ala267Pro	missense_variant	Exon 9 of 23	1	NM_015099.4	ENSP00000321813.7		O94983-1

Frequencies

GnomAD3 genomes

AF:

0.816

AC:

117544

AN:

144116

Hom.:

48688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.933

Gnomad AMI

AF:

0.751

Gnomad AMR

AF:

0.831

Gnomad ASJ

AF:

0.740

Gnomad EAS

AF:

0.483

Gnomad SAS

AF:

0.503

Gnomad FIN

AF:

0.699

Gnomad MID

AF:

0.842

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.829

GnomAD3 exomes

AF:

0.748

AC:

185915

AN:

248402

Hom.:

71657

AF XY:

0.737

AC XY:

99413

AN XY:

134884

show subpopulations

Gnomad AFR exome

AF:

0.938

Gnomad AMR exome

AF:

0.810

Gnomad ASJ exome

AF:

0.743

Gnomad EAS exome

AF:

0.493

Gnomad SAS exome

AF:

0.509

Gnomad FIN exome

AF:

0.712

Gnomad NFE exome

AF:

0.815

Gnomad OTH exome

AF:

0.779

GnomAD4 exome

AF:

0.784

AC:

1141339

AN:

1455794

Hom.:

453609

Cov.:

AF XY:

0.776

AC XY:

562149

AN XY:

724316

show subpopulations

Gnomad4 AFR exome

AF:

0.939

Gnomad4 AMR exome

AF:

0.811

Gnomad4 ASJ exome

AF:

0.749

Gnomad4 EAS exome

AF:

0.496

Gnomad4 SAS exome

AF:

0.525

Gnomad4 FIN exome

AF:

0.724

Gnomad4 NFE exome

AF:

0.813

Gnomad4 OTH exome

AF:

0.773

GnomAD4 genome

AF:

0.816

AC:

117677

AN:

144230

Hom.:

48756

Cov.:

AF XY:

0.806

AC XY:

56216

AN XY:

69740

show subpopulations

Gnomad4 AFR

AF:

0.933

Gnomad4 AMR

AF:

0.831

Gnomad4 ASJ

AF:

0.740

Gnomad4 EAS

AF:

0.483

Gnomad4 SAS

AF:

0.505

Gnomad4 FIN

AF:

0.699

Gnomad4 NFE

AF:

0.811

Gnomad4 OTH

AF:

0.828

Alfa

AF:

0.794

Hom.:

32898

Bravo

AF:

0.835

TwinsUK

AF:

0.799

AC:

2963

ALSPAC

AF:

0.806

AC:

3107

ESP6500AA

AF:

0.937

AC:

3851

ESP6500EA

AF:

0.807

AC:

6766

ExAC

AF:

0.751

AC:

90790

EpiCase

AF:

0.807

EpiControl

AF:

0.817

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jan 18, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 26886562) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.051

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.43

DANN

Benign

0.51

DEOGEN2

Benign

0.0070

.;.;T;.;T

Eigen

Benign

-2.3

Eigen_PC

Benign

-2.2

FATHMM_MKL

Benign

0.0037

LIST_S2

Benign

0.038

T;T;T;T;T

MetaRNN

Benign

7.4e-7

T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.55

.;.;.;.;N

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.040

N;N;.;N;N

REVEL

Benign

0.044

Sift

Benign

1.0

T;T;.;T;T

Sift4G

Benign

0.15

T;T;T;T;T

Polyphen

0.0

.;B;.;B;B

Vest4

0.026

MPC

0.28

ClinPred

0.0015

GERP RS

-2.1

Varity_R

0.035

gMVP

0.30

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over