rs11868948

Positions:

• chr17-10310725-G-A

Variant summary

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

The NM_003802.3(MYH13):​c.4656+378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,886 control chromosomes in the GnomAD database, including 31,145 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 0.64 (31145 hom., cov: 31)
• Consequence: MYH13 NM_003802.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH13	NM_003802.3	c.4656+378C>T		intron_variant		ENST00000252172.9
LOC107985004	XR_007065617.1	n.96-6773G>A		intron_variant, non_coding_transcript_variant
LOC107985004	XR_001752791.3	n.96-6773G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH13	ENST00000252172.9	c.4656+378C>T		intron_variant		1	NM_003802.3	P1
MYH13	ENST00000621918.1	c.4656+378C>T		intron_variant		1		P1
	ENST00000609088.1	n.95-6773G>A		intron_variant, non_coding_transcript_variant		4
MYH13	ENST00000418404.8	c.4656+378C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96573 AN: 151768 Hom.: 31116 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.636 AC: 96653 AN: 151886 Hom.: 31145 Cov.: 31 AF XY: 0.628 AC XY: 46618 AN XY: 74222

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.616

Alfa AF: 0.621 Hom.: 38642

Bravo AF: 0.648

Asia WGS AF: 0.487 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.65

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: rs11868948; hg19: chr17-10214042;