ENST00000399342.6:n.76+1299C>T

Variant names:

• chr17-10384506-C-T
• rs9906430
• ENST00000399342.6:n.76+1299C>T

Variant summary

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

The ENST00000399342.6(MYHAS):​n.76+1299C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,958 control chromosomes in the GnomAD database, including 15,813 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 0.45 (15813 hom., cov: 31)
• Consequence: MYHAS ENST00000399342.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYHAS	NR_125367.1	n.76+1299C>T		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYHAS	ENST00000399342.6	n.76+1299C>T		intron_variant	Intron 1 of 3	3
MYHAS	ENST00000581304.2	n.52+1299C>T		intron_variant	Intron 1 of 4	3
MYHAS	ENST00000584139.2	n.440-21642C>T		intron_variant	Intron 3 of 8	3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67722 AN: 151840 Hom.: 15808 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.446 AC: 67763 AN: 151958 Hom.: 15813 Cov.: 31 AF XY: 0.436 AC XY: 32392 AN XY: 74250

African (AFR) AF: 0.367 AC: 15213 AN: 41438

American (AMR) AF: 0.414 AC: 6325 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3470

East Asian (EAS) AF: 0.143 AC: 740 AN: 5172

South Asian (SAS) AF: 0.254 AC: 1227 AN: 4824

European-Finnish (FIN) AF: 0.500 AC: 5273 AN: 10546

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35931 AN: 67936

Other (OTH) AF: 0.461 AC: 972 AN: 2108

Alfa AF: 0.391 Hom.: 1688

Bravo AF: 0.440

Asia WGS AF: 0.242 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.71
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs9906430; hg19: chr17-10287823;