chr5-79729078-G-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_153610.5(CMYA5):āc.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
NM_153610.5 missense
Scores
4
5
10
Clinical Significance
Conservation
PhyloP100: 7.25
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 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 |
---|---|---|---|---|---|---|---|---|
CMYA5 | NM_153610.5 | c.313G>C | p.Gly105Arg | missense_variant | 2/13 | ENST00000446378.3 | NP_705838.3 | |
CMYA5 | XM_047416911.1 | c.313G>C | p.Gly105Arg | missense_variant | 2/6 | XP_047272867.1 | ||
CMYA5 | XR_001742036.3 | n.385G>C | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CMYA5 | ENST00000446378.3 | c.313G>C | p.Gly105Arg | missense_variant | 2/13 | 5 | NM_153610.5 | ENSP00000394770 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00169 AC: 257AN: 152106Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000530 AC: 132AN: 249126Hom.: 0 AF XY: 0.000355 AC XY: 48AN XY: 135152
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GnomAD4 exome AF: 0.000198 AC: 289AN: 1461676Hom.: 1 Cov.: 33 AF XY: 0.000173 AC XY: 126AN XY: 727120
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GnomAD4 genome AF: 0.00169 AC: 258AN: 152224Hom.: 1 Cov.: 32 AF XY: 0.00176 AC XY: 131AN XY: 74420
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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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 27, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
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T
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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