17-10366197-C-T

Position:

• chr17-10366197-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.-12-1655G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,150 control chromosomes in the GnomAD database, including 13,080 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 0.40 (13080 hom., cov: 28)
• Consequence: MYH13 NM_003802.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYH13	NM_003802.3	c.-12-1655G>A		intron_variant		ENST00000252172.9	NP_003793.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYH13	ENST00000252172.9	c.-12-1655G>A		intron_variant		1	NM_003802.3	ENSP00000252172.4
MYH13	ENST00000418404.8	c.-12-1655G>A		intron_variant		5		ENSP00000404570.3

Frequencies

GnomAD3 genomes AF: 0.403 AC: 60922 AN: 151032 Hom.: 13081 Cov.: 28

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.403 AC: 60943 AN: 151150 Hom.: 13080 Cov.: 28 AF XY: 0.399 AC XY: 29461 AN XY: 73792

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.421

Alfa AF: 0.467 Hom.: 17017

Bravo AF: 0.391

Asia WGS AF: 0.265 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs12936065; hg19: chr17-10269514;