chr5-79729205-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_153610.5(CMYA5):c.440G>A(p.Arg147Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00406 in 1,612,770 control chromosomes in the GnomAD database, including 245 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 130 hom., cov: 33)
Exomes 𝑓: 0.0022 ( 115 hom. )
Consequence
CMYA5
NM_153610.5 missense
NM_153610.5 missense
Scores
1
6
11
Clinical Significance
Conservation
PhyloP100: 1.63
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0025502741).
BP6
?
Variant 5-79729205-G-A is Benign according to our data. Variant chr5-79729205-G-A is described in ClinVar as [Benign]. Clinvar id is 785129.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0744 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CMYA5 | NM_153610.5 | c.440G>A | p.Arg147Gln | missense_variant | 2/13 | ENST00000446378.3 | |
CMYA5 | XM_047416911.1 | c.440G>A | p.Arg147Gln | missense_variant | 2/6 | ||
CMYA5 | XR_001742036.3 | n.512G>A | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CMYA5 | ENST00000446378.3 | c.440G>A | p.Arg147Gln | missense_variant | 2/13 | 5 | NM_153610.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0218 AC: 3322AN: 152086Hom.: 130 Cov.: 33
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GnomAD3 exomes AF: 0.00542 AC: 1342AN: 247774Hom.: 49 AF XY: 0.00412 AC XY: 554AN XY: 134352
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GnomAD4 exome AF: 0.00221 AC: 3230AN: 1460566Hom.: 115 Cov.: 34 AF XY: 0.00191 AC XY: 1387AN XY: 726516
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GnomAD4 genome ? AF: 0.0218 AC: 3325AN: 152204Hom.: 130 Cov.: 33 AF XY: 0.0209 AC XY: 1555AN XY: 74420
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at