chr17-10342368-C-T

Variant names:

• chr17-10342368-C-T
• rs11869897
• NM_003802.3:c.1894+1432G>A

Variant summary

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

The ENST00000252172.9(MYH13):​c.1894+1432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,992 control chromosomes in the GnomAD database, including 4,743 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 0.24 (4743 hom., cov: 32)
• Consequence: MYH13 ENST00000252172.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 1 publications found

Genes affected

MYH13 (HGNC:7571): (myosin heavy chain 13) Predicted to enable microfilament motor activity. Predicted to be involved in muscle contraction. Predicted to act upstream of or within cellular response to starvation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000252172.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYH13	NM_003802.3	MANE Select	c.1894+1432G>A		intron	N/A	NP_003793.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYH13	ENST00000252172.9	TSL:1 MANE Select	c.1894+1432G>A		intron	N/A	ENSP00000252172.4
	MYH13	ENST00000621918.1	TSL:1	c.1894+1432G>A		intron	N/A	ENSP00000480864.1
	MYH13	ENST00000418404.8	TSL:5	c.1894+1432G>A		intron	N/A	ENSP00000404570.3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35975 AN: 151874 Hom.: 4722 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.237 AC: 36053 AN: 151992 Hom.: 4743 Cov.: 32 AF XY: 0.243 AC XY: 18082 AN XY: 74278

African (AFR) AF: 0.277 AC: 11461 AN: 41428

American (AMR) AF: 0.254 AC: 3883 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2887 AN: 5160

South Asian (SAS) AF: 0.313 AC: 1504 AN: 4804

European-Finnish (FIN) AF: 0.205 AC: 2162 AN: 10566

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12742 AN: 67994

Other (OTH) AF: 0.223 AC: 469 AN: 2106

Alfa AF: 0.181 Hom.: 1073

Bravo AF: 0.243

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.51
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11869897; hg19: chr17-10245685;