5-79726888-C-G

Variant names:

• chr5-79726888-C-G
• rs6880680
• NM_153610.5:c.150-2027C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153610.5(CMYA5):​c.150-2027C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 147,420 control chromosomes in the GnomAD database, including 6,007 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (6007 hom., cov: 30)
• Consequence: CMYA5 NM_153610.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMYA5	NM_153610.5	c.150-2027C>G		intron_variant	Intron 1 of 12	ENST00000446378.3	NP_705838.3
CMYA5	XM_047416911.1	c.150-2027C>G		intron_variant	Intron 1 of 5		XP_047272867.1
CMYA5	XR_001742036.3	n.222-2027C>G		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMYA5	ENST00000446378.3	c.150-2027C>G		intron_variant	Intron 1 of 12	5	NM_153610.5	ENSP00000394770.2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 31117 AN: 147344 Hom.: 5984 Cov.: 30

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.0122

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0877

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.183

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.212 AC: 31186 AN: 147420 Hom.: 6007 Cov.: 30 AF XY: 0.211 AC XY: 15119 AN XY: 71672

African (AFR) AF: 0.508 AC: 19875 AN: 39132

American (AMR) AF: 0.0987 AC: 1474 AN: 14934

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 346 AN: 3448

East Asian (EAS) AF: 0.391 AC: 1922 AN: 4916

South Asian (SAS) AF: 0.103 AC: 481 AN: 4682

European-Finnish (FIN) AF: 0.102 AC: 984 AN: 9654

Middle Eastern (MID) AF: 0.0915 AC: 26 AN: 284

European-Non Finnish (NFE) AF: 0.0845 AC: 5695 AN: 67422

Other (OTH) AF: 0.182 AC: 372 AN: 2044

Alfa AF: 0.149 Hom.: 362

Bravo AF: 0.234

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6880680; hg19: chr5-79022711; COSMIC: COSV71404750;