rs56157640

chr5-127455564-G-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_001256545.2(MEGF10):c.3189G>A(p.Glu1063=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 1,614,078 control chromosomes in the GnomAD database, including 602 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.019 (54 hom., cov: 32)
  • Exomes 𝑓: 0.022 (548 hom.)
• Consequence: MEGF10 NM_001256545.2 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 1.59

Genes affected

MEGF10 (HGNC:29634): (multiple EGF like domains 10) This gene encodes a member of the multiple epidermal growth factor-like domains protein family. The encoded protein plays a role in cell adhesion, motility and proliferation, and is a critical mediator of apoptotic cell phagocytosis as well as amyloid-beta peptide uptake in the brain. Expression of this gene may be associated with schizophrenia, and mutations in this gene are a cause of early-onset myopathy, areflexia, respiratory distress, and dysphagia (EMARDD) as well as congenital myopathy with minicores. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP6: Variant 5-127455564-G-A is Benign according to our data. Variant chr5-127455564-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 380909.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.59 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEGF10	NM_001256545.2	c.3189G>A	p.Glu1063=	synonymous_variant	24/25	ENST00000503335.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEGF10	ENST00000503335.7	c.3189G>A	p.Glu1063=	synonymous_variant	24/25	1	NM_001256545.2	P1
MEGF10	ENST00000274473.6	c.3189G>A	p.Glu1063=	synonymous_variant	25/26	1		P1
MEGF10	ENST00000515622.1	n.390G>A		non_coding_transcript_exon_variant	4/5	2
MEGF10	ENST00000510828.5			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 2849 AN: 152136 Hom.: 53 Cov.: 32

Gnomad AFR AF: 0.00674

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0109

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0201

GnomAD3 exomes AF: 0.0266 AC: 6667 AN: 251088 Hom.: 155 AF XY: 0.0291 AC XY: 3956 AN XY: 135716

Gnomad AFR exome AF: 0.00517

Gnomad AMR exome AF: 0.0111

Gnomad ASJ exome AF: 0.0466

Gnomad EAS exome AF: 0.0500

Gnomad SAS exome AF: 0.0664

Gnomad FIN exome AF: 0.0293

Gnomad NFE exome AF: 0.0175

Gnomad OTH exome AF: 0.0262

GnomAD4 exome AF: 0.0218 AC: 31891 AN: 1461824 Hom.: 548 Cov.: 31 AF XY: 0.0231 AC XY: 16829 AN XY: 727218

Gnomad4 AFR exome AF: 0.00511

Gnomad4 AMR exome AF: 0.0105

Gnomad4 ASJ exome AF: 0.0454

Gnomad4 EAS exome AF: 0.0387

Gnomad4 SAS exome AF: 0.0661

Gnomad4 FIN exome AF: 0.0293

Gnomad4 NFE exome AF: 0.0176

Gnomad4 OTH exome AF: 0.0252

GnomAD4 genome AF: 0.0187 AC: 2846 AN: 152254 Hom.: 54 Cov.: 32 AF XY: 0.0206 AC XY: 1530 AN XY: 74442

Gnomad4 AFR AF: 0.00672

Gnomad4 AMR AF: 0.0108

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.0500

Gnomad4 SAS AF: 0.0777

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0187 Hom.: 18

Bravo AF: 0.0153

Asia WGS AF: 0.0500 AC: 173 AN: 3478

EpiCase AF: 0.0182

EpiControl AF: 0.0156

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 29, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 2.7% of total chromosomes in ExAC, 6.8% of S. Asian chromosomes -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 10, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

MEGF10-related myopathy Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	5.5
Dann	Benign	0.47

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: rs56157640; hg19: chr5-126791256;