rs11654423

Variant names:

• chr17-10442014-C-T
• rs11654423
• ENST00000399342.6:n.206+35737C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000399342.6(ENSG00000272736):​n.206+35737C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,950 control chromosomes in the GnomAD database, including 8,938 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 0.32 (8938 hom., cov: 32)
• Consequence: ENSG00000272736 ENST00000399342.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

ENSG00000272736 (HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYHAS	NR_125367.1	n.167+35776C>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272736	ENST00000399342.6	n.206+35737C>T		intron_variant	Intron 2 of 3	3
ENSG00000272736	ENST00000581304.1	n.143+35776C>T		intron_variant	Intron 2 of 3	3
MYHAS	ENST00000587182.2	n.155+35776C>T		intron_variant	Intron 2 of 10	5

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48659 AN: 151832 Hom.: 8941 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.320 AC: 48679 AN: 151950 Hom.: 8938 Cov.: 32 AF XY: 0.333 AC XY: 24729 AN XY: 74254

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.298

Alfa AF: 0.302 Hom.: 5880

Bravo AF: 0.317

Asia WGS AF: 0.580 AC: 2010 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11654423; hg19: chr17-10345331;