rs11651414

Positions:

• chr17-10348494-A-G

Variant summary

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

The NM_003802.3(MYH13):​c.1145-1696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,098 control chromosomes in the GnomAD database, including 12,940 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 0.38 (12940 hom., cov: 32)
• Consequence: MYH13 NM_003802.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH13	NM_003802.3	c.1145-1696T>C		intron_variant		ENST00000252172.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH13	ENST00000252172.9	c.1145-1696T>C		intron_variant		1	NM_003802.3	P1
MYH13	ENST00000621918.1	c.1145-1696T>C		intron_variant		1		P1
MYH13	ENST00000418404.8	c.1145-1696T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57223 AN: 151980 Hom.: 12946 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.376 AC: 57214 AN: 152098 Hom.: 12940 Cov.: 32 AF XY: 0.372 AC XY: 27672 AN XY: 74344

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.415

Alfa AF: 0.485 Hom.: 17329

Bravo AF: 0.360

Asia WGS AF: 0.229 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.19

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: rs11651414; hg19: chr17-10251811;