rs8077200

Variant names:

• chr17-10486966-A-G
• rs8077200
• ENST00000399342.6:n.207-46358A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-10486966-A-G
• chr17-10486966-A-T

Variant summary

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

The ENST00000399342.6(ENSG00000272736):​n.207-46358A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,870 control chromosomes in the GnomAD database, including 14,502 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 (14502 hom., cov: 32)
• Consequence: ENSG00000272736 ENST00000399342.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYHAS	NR_125367.1	n.168-80571A>G		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272736	ENST00000399342.6	n.207-46358A>G		intron_variant	Intron 2 of 3	3
ENSG00000272736	ENST00000581304.1	n.144-46358A>G		intron_variant	Intron 2 of 3	3
MYHAS	ENST00000587182.2	n.156-80571A>G		intron_variant	Intron 2 of 10	5

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64136 AN: 151752 Hom.: 14494 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.423 AC: 64182 AN: 151870 Hom.: 14502 Cov.: 32 AF XY: 0.436 AC XY: 32342 AN XY: 74226

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.393

Alfa AF: 0.395 Hom.: 1749

Bravo AF: 0.415

Asia WGS AF: 0.687 AC: 2387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8077200; hg19: chr17-10390283;