rs11071868

chr15-66183864-G-A

Variant summary

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

The NM_001385028.1(MEGF11):c.-8-55453C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,036 control chromosomes in the GnomAD database, including 4,161 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 0.22 (4161 hom., cov: 31)
• Consequence: MEGF11 NM_001385028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

MEGF11 (HGNC:29635): (multiple EGF like domains 11) Predicted to be involved in homotypic cell-cell adhesion and retina layer formation. Predicted to be located in basolateral plasma membrane. Predicted to be integral component of membrane. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEGF11	NM_001385028.1	c.-8-55453C>T		intron_variant		ENST00000395614.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEGF11	ENST00000395614.6	c.-8-55453C>T		intron_variant		5	NM_001385028.1	A1
MEGF11	ENST00000288745.7	c.-26-59864C>T		intron_variant		1
MEGF11	ENST00000422354.6	c.-8-55453C>T		intron_variant		1		P2
MEGF11	ENST00000409699.6	c.-30-55431C>T		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33643 AN: 151918 Hom.: 4161 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.221 AC: 33659 AN: 152036 Hom.: 4161 Cov.: 31 AF XY: 0.225 AC XY: 16701 AN XY: 74314

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.215

Alfa AF: 0.209 Hom.: 3856

Bravo AF: 0.222

Asia WGS AF: 0.324 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.63

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: rs11071868; hg19: chr15-66476202;