17-10520523-T-C

Variant names:

• chr17-10520523-T-C
• rs9916035
• ENST00000399342.6:n.207-12801T>C

Variant summary

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

The ENST00000399342.6(MYHAS):​n.207-12801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,038 control chromosomes in the GnomAD database, including 14,281 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 0.42 (14281 hom., cov: 32)
• Consequence: MYHAS ENST00000399342.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.19
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399342.6. 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
	MYHAS	NR_125367.1		n.168-47014T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYHAS	ENST00000399342.6	TSL:3	n.207-12801T>C		intron	N/A
	MYHAS	ENST00000581304.2	TSL:3	n.144-12801T>C		intron	N/A
	MYHAS	ENST00000584139.2	TSL:3	n.531-87831T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63734 AN: 151920 Hom.: 14265 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.420 AC: 63796 AN: 152038 Hom.: 14281 Cov.: 32 AF XY: 0.431 AC XY: 32053 AN XY: 74302

African (AFR) AF: 0.331 AC: 13708 AN: 41468

American (AMR) AF: 0.492 AC: 7511 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.861 AC: 4450 AN: 5166

South Asian (SAS) AF: 0.619 AC: 2974 AN: 4808

European-Finnish (FIN) AF: 0.450 AC: 4762 AN: 10574

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27420 AN: 67964

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.388 Hom.: 1654

Bravo AF: 0.417

Asia WGS AF: 0.684 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.30
PhyloP100		-6.2

Splicing

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

Other links and lift over

dbSNP: rs9916035; hg19: chr17-10423840; COSMIC: COSV55434300;