5-79695550-A-G

Variant names:

• chr5-79695550-A-G
• rs6883197
• NM_153610.5:c.149+5494A>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.149+5494A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,058 control chromosomes in the GnomAD database, including 16,381 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 0.43 (16381 hom., cov: 32)
• Consequence: CMYA5 NM_153610.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153610.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMYA5	NM_153610.5	MANE Select	c.149+5494A>G		intron	N/A	NP_705838.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMYA5	ENST00000446378.3	TSL:5 MANE Select	c.149+5494A>G		intron	N/A	ENSP00000394770.2	Q8N3K9
	CMYA5	ENST00000940891.1		c.149+5494A>G		intron	N/A	ENSP00000610950.1
	CMYA5	ENST00000856934.1		c.150-89A>G		intron	N/A	ENSP00000526993.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65954 AN: 151940 Hom.: 16327 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.434 AC: 66069 AN: 152058 Hom.: 16381 Cov.: 32 AF XY: 0.435 AC XY: 32364 AN XY: 74320

African (AFR) AF: 0.687 AC: 28494 AN: 41468

American (AMR) AF: 0.463 AC: 7072 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1450 AN: 5164

South Asian (SAS) AF: 0.378 AC: 1820 AN: 4820

European-Finnish (FIN) AF: 0.352 AC: 3729 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21308 AN: 67976

Other (OTH) AF: 0.390 AC: 824 AN: 2112

Alfa AF: 0.269 Hom.: 1052

Bravo AF: 0.455

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.27
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: rs6883197; hg19: chr5-78991373;