rs7213488

Variant names:

• chr17-10376626-G-T
• rs7213488
• ENST00000584139.2:n.440-29522G>T

Variant summary

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

The ENST00000584139.2(MYHAS):​n.440-29522G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,912 control chromosomes in the GnomAD database, including 6,211 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 0.28 (6211 hom., cov: 31)
• Consequence: MYHAS ENST00000584139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYHAS	ENST00000584139.2	n.440-29522G>T		intron_variant	Intron 3 of 8	3
MYHAS	ENST00000715356.1	n.216-29522G>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42142 AN: 151794 Hom.: 6207 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.278 AC: 42165 AN: 151912 Hom.: 6211 Cov.: 31 AF XY: 0.271 AC XY: 20104 AN XY: 74232

African (AFR) AF: 0.249 AC: 10322 AN: 41400

American (AMR) AF: 0.249 AC: 3802 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3470

East Asian (EAS) AF: 0.0350 AC: 181 AN: 5174

South Asian (SAS) AF: 0.134 AC: 646 AN: 4824

European-Finnish (FIN) AF: 0.294 AC: 3102 AN: 10540

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.322 AC: 21886 AN: 67954

Other (OTH) AF: 0.280 AC: 589 AN: 2104

Alfa AF: 0.304 Hom.: 13252

Bravo AF: 0.275

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7213488; hg19: chr17-10279943;