ENST00000584139.2:n.531-55539G>T

Variant names:

• chr17-10552815-G-T
• rs4239117
• ENST00000584139.2:n.531-55539G>T

Variant summary

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

The ENST00000584139.2(MYHAS):​n.531-55539G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,874 control chromosomes in the GnomAD database, including 10,454 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 0.35 (10454 hom., cov: 31)
• Consequence: MYHAS ENST00000584139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 1 publications found

Genes affected

MYHAS (HGNC:50609): (myosin heavy chain gene cluster antisense RNA) Predicted to enable primary miRNA binding activity. Predicted to be involved in response to muscle activity and skeletal muscle fiber development. Predicted to act upstream of or within with a positive effect on gene expression. Predicted to be located in cytoplasm and nucleus. [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 (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYHAS	NR_125367.1	n.168-14722G>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYHAS	ENST00000584139.2	n.531-55539G>T		intron_variant	Intron 4 of 8	3
MYHAS	ENST00000587182.3	n.156-14722G>T		intron_variant	Intron 2 of 10	5
MYHAS	ENST00000715356.1	n.307-55539G>T		intron_variant	Intron 3 of 6
MYHAS	ENST00000850668.1	n.170-45258G>T		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53647 AN: 151756 Hom.: 10455 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.353 AC: 53669 AN: 151874 Hom.: 10454 Cov.: 31 AF XY: 0.364 AC XY: 26999 AN XY: 74186

African (AFR) AF: 0.246 AC: 10205 AN: 41416

American (AMR) AF: 0.443 AC: 6766 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3468

East Asian (EAS) AF: 0.805 AC: 4137 AN: 5136

South Asian (SAS) AF: 0.493 AC: 2363 AN: 4792

European-Finnish (FIN) AF: 0.397 AC: 4194 AN: 10554

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.347 AC: 23547 AN: 67922

Other (OTH) AF: 0.338 AC: 714 AN: 2112

Alfa AF: 0.325 Hom.: 1232

Bravo AF: 0.352

Asia WGS AF: 0.577 AC: 2003 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	0.14
DANN	Benign	0.77
PhyloP100		-0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4239117; hg19: chr17-10456132; COSMIC: COSV55434443;