ENST00000584139.2:n.440-32819T>C

Variant names:

• chr17-10373329-T-C
• rs3809738
• ENST00000584139.2:n.440-32819T>C

Variant summary

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

The ENST00000584139.2(MYHAS):​n.440-32819T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,120 control chromosomes in the GnomAD database, including 1,127 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 0.11 (1127 hom., cov: 32)
• Consequence: MYHAS ENST00000584139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 5 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]

MYH13 (HGNC:7571): (myosin heavy chain 13) Predicted to enable microfilament motor activity. Predicted to be involved in muscle contraction. Predicted to act upstream of or within cellular response to starvation. Located in extracellular exosome. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584139.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYHAS	ENST00000584139.2	TSL:3	n.440-32819T>C		intron	N/A
	MYHAS	ENST00000715356.1		n.216-32819T>C		intron	N/A
	MYH13	ENST00000418404.8	TSL:5	c.-363A>G		upstream_gene	N/A	ENSP00000404570.3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16830 AN: 152002 Hom.: 1123 Cov.: 32

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0938

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.111 AC: 16840 AN: 152120 Hom.: 1127 Cov.: 32 AF XY: 0.110 AC XY: 8193 AN XY: 74368

African (AFR) AF: 0.0300 AC: 1246 AN: 41512

American (AMR) AF: 0.141 AC: 2162 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 325 AN: 3464

East Asian (EAS) AF: 0.144 AC: 743 AN: 5170

South Asian (SAS) AF: 0.133 AC: 644 AN: 4826

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10574

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9895 AN: 67964

Other (OTH) AF: 0.0858 AC: 181 AN: 2110

Alfa AF: 0.126 Hom.: 2716

Bravo AF: 0.110

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		1.1
PromoterAI		0.00040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3809738; hg19: chr17-10276646;