Variant chr5-79690010-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_153610.5(CMYA5):c.103G>A(p.Glu35Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,484,580 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0031 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 71 hom. )

Consequence

CMYA5
NM_153610.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.33

Variant links:

Genes affected

CMYA5 (HGNC:14305): (cardiomyopathy associated 5) Predicted to enable identical protein binding activity. Predicted to act upstream of or within negative regulation of calcineurin-NFAT signaling cascade; negative regulation of phosphoprotein phosphatase activity; and regulation of skeletal muscle adaptation. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CMYA5 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=0.004689783).

BP6

Variant 5-79690010-G-A is Benign according to our data. Variant chr5-79690010-G-A is described in ClinVar as [Benign]. Clinvar id is 791626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CMYA5	NM_153610.5 linkuse as main transcript	c.103G>A	p.Glu35Lys	missense_variant	1/13	ENST00000446378.3
CMYA5	XM_047416911.1 linkuse as main transcript	c.103G>A	p.Glu35Lys	missense_variant	1/6
CMYA5	XR_001742036.3 linkuse as main transcript	n.175G>A		non_coding_transcript_exon_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMYA5	ENST00000446378.3 linkuse as main transcript	c.103G>A	p.Glu35Lys	missense_variant	1/13	5	NM_153610.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00306

AC:

466

AN:

152230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000555

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0477

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00301

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00170

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00401

AC:

391

AN:

97422

Hom.:

AF XY:

0.00374

AC XY:

194

AN XY:

51922

show subpopulations

Gnomad AFR exome

AF:

0.000317

Gnomad AMR exome

AF:

0.00118

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0443

Gnomad SAS exome

AF:

0.00205

Gnomad FIN exome

AF:

0.00292

Gnomad NFE exome

AF:

0.00179

Gnomad OTH exome

AF:

0.00296

GnomAD4 exome

AF:

0.00303

AC:

4037

AN:

1332232

Hom.:

Cov.:

AF XY:

0.00295

AC XY:

1937

AN XY:

655614

show subpopulations

Gnomad4 AFR exome

AF:

0.000406

Gnomad4 AMR exome

AF:

0.00138

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0563

Gnomad4 SAS exome

AF:

0.00208

Gnomad4 FIN exome

AF:

0.00321

Gnomad4 NFE exome

AF:

0.00173

Gnomad4 OTH exome

AF:

0.00259

GnomAD4 genome

AF:

0.00306

AC:

466

AN:

152348

Hom.:

Cov.:

AF XY:

0.00357

AC XY:

266

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.000553

Gnomad4 AMR

AF:

0.00176

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0478

Gnomad4 SAS

AF:

0.00269

Gnomad4 FIN

AF:

0.00301

Gnomad4 NFE

AF:

0.00170

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00139

Hom.:

Bravo

AF:

0.00361

ESP6500AA

AF:

0.000288

AC:

ESP6500EA

AF:

0.00130

AC:

ExAC

AF:

0.00200

AC:

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 28, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.45

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.020

Eigen

Benign

0.074

Eigen_PC

Benign

0.053

FATHMM_MKL

Benign

0.76

LIST_S2

Benign

0.67

MetaRNN

Benign

0.0047

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.55

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.66

PROVEAN

Benign

-1.6

REVEL

Benign

0.070

Sift

Uncertain

0.0050

Sift4G

Uncertain

0.054

Polyphen

0.98

Vest4

0.26

MVP

0.34

MPC

0.24

ClinPred

0.033

GERP RS

3.2

Varity_R

0.31

gMVP

0.12

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over