rs11651414

Variant names:

• chr17-10348494-A-G
• rs11651414
• NM_003802.3:c.1145-1696T>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-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 rank	MANE	Protein	UniProt
MYH13	NM_003802.3	c.1145-1696T>C		intron_variant	Intron 12 of 40	ENST00000252172.9	NP_003793.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH13	ENST00000252172.9	c.1145-1696T>C		intron_variant	Intron 12 of 40	1	NM_003802.3	ENSP00000252172.4

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

African (AFR) AF: 0.133 AC: 5516 AN: 41502

American (AMR) AF: 0.397 AC: 6064 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5172

South Asian (SAS) AF: 0.255 AC: 1233 AN: 4826

European-Finnish (FIN) AF: 0.495 AC: 5235 AN: 10570

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 35028 AN: 67964

Other (OTH) AF: 0.415 AC: 876 AN: 2110

Alfa AF: 0.467 Hom.: 21926

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
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11651414; hg19: chr17-10251811;