5-79729078-G-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_153610.5(CMYA5):ā€‹c.313G>Cā€‹(p.Gly105Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000339 in 1,613,900 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.0017 ( 1 hom., cov: 32)
Exomes š‘“: 0.00020 ( 1 hom. )

Consequence

CMYA5
NM_153610.5 missense

Scores

4
5
10

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.25
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0073223114).
BP6
Variant 5-79729078-G-C is Benign according to our data. Variant chr5-79729078-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 716935.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CMYA5NM_153610.5 linkuse as main transcriptc.313G>C p.Gly105Arg missense_variant 2/13 ENST00000446378.3 NP_705838.3
CMYA5XM_047416911.1 linkuse as main transcriptc.313G>C p.Gly105Arg missense_variant 2/6 XP_047272867.1
CMYA5XR_001742036.3 linkuse as main transcriptn.385G>C non_coding_transcript_exon_variant 2/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CMYA5ENST00000446378.3 linkuse as main transcriptc.313G>C p.Gly105Arg missense_variant 2/135 NM_153610.5 ENSP00000394770 P1

Frequencies

GnomAD3 genomes
AF:
0.00169
AC:
257
AN:
152106
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00594
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000957
GnomAD3 exomes
AF:
0.000530
AC:
132
AN:
249126
Hom.:
0
AF XY:
0.000355
AC XY:
48
AN XY:
135152
show subpopulations
Gnomad AFR exome
AF:
0.00736
Gnomad AMR exome
AF:
0.000377
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000177
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000198
AC:
289
AN:
1461676
Hom.:
1
Cov.:
33
AF XY:
0.000173
AC XY:
126
AN XY:
727120
show subpopulations
Gnomad4 AFR exome
AF:
0.00699
Gnomad4 AMR exome
AF:
0.000313
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.000414
GnomAD4 genome
AF:
0.00169
AC:
258
AN:
152224
Hom.:
1
Cov.:
32
AF XY:
0.00176
AC XY:
131
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.00595
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000947
Alfa
AF:
0.000172
Hom.:
0
Bravo
AF:
0.00193
ESP6500AA
AF:
0.00773
AC:
29
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000546
AC:
66
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 27, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.42
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.32
CADD
Pathogenic
26
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.037
T
Eigen
Pathogenic
0.70
Eigen_PC
Pathogenic
0.74
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.83
T
M_CAP
Benign
0.052
D
MetaRNN
Benign
0.0073
T
MetaSVM
Benign
-0.73
T
MutationAssessor
Benign
1.4
L
MutationTaster
Benign
0.90
D
PrimateAI
Benign
0.40
T
PROVEAN
Uncertain
-4.2
D
REVEL
Uncertain
0.31
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.021
D
Polyphen
1.0
D
Vest4
0.36
MVP
0.63
MPC
0.38
ClinPred
0.059
T
GERP RS
5.6
Varity_R
0.38
gMVP
0.14

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.

Other links and lift over

dbSNP: rs147271727; hg19: chr5-79024901; API