chr5-79698539-C-T

Variant names:

• chr5-79698539-C-T
• rs9784710
• NM_153610.5:c.149+8483C>T

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+8483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,142 control chromosomes in the GnomAD database, including 1,902 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 0.16 (1902 hom., cov: 32)
• Consequence: CMYA5 NM_153610.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMYA5	NM_153610.5	c.149+8483C>T		intron_variant	Intron 1 of 12	ENST00000446378.3	NP_705838.3
CMYA5	XM_047416911.1	c.149+8483C>T		intron_variant	Intron 1 of 5		XP_047272867.1
CMYA5	XR_001742036.3	n.221+8483C>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMYA5	ENST00000446378.3	c.149+8483C>T		intron_variant	Intron 1 of 12	5	NM_153610.5	ENSP00000394770.2

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23600 AN: 152024 Hom.: 1892 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.155 AC: 23640 AN: 152142 Hom.: 1902 Cov.: 32 AF XY: 0.153 AC XY: 11360 AN XY: 74372

African (AFR) AF: 0.197 AC: 8158 AN: 41474

American (AMR) AF: 0.116 AC: 1768 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 480 AN: 3470

East Asian (EAS) AF: 0.0353 AC: 183 AN: 5180

South Asian (SAS) AF: 0.143 AC: 689 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1330 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10458 AN: 68000

Other (OTH) AF: 0.149 AC: 315 AN: 2116

Alfa AF: 0.149 Hom.: 3126

Bravo AF: 0.157

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.19
PhyloP100		0.076
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: rs9784710; hg19: chr5-78994362;