chr17-10342368-C-T

Position:

• chr17-10342368-C-T

Variant summary

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

The NM_003802.3(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 NM_003802.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH13	NM_003802.3	c.1894+1432G>A		intron_variant		ENST00000252172.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH13	ENST00000252172.9	c.1894+1432G>A		intron_variant		1	NM_003802.3	P1
MYH13	ENST00000621918.1	c.1894+1432G>A		intron_variant		1		P1
MYH13	ENST00000418404.8	c.1894+1432G>A		intron_variant		5		P1

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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.223

Alfa AF: 0.162 Hom.: 548

Bravo AF: 0.243

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs11869897; hg19: chr17-10245685;