rs10760112

chr9-120705292-C-T

Variant summary

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

The NM_001080497.3(MEGF9):c.601+8466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,476 control chromosomes in the GnomAD database, including 28,594 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 0.58 (28594 hom., cov: 30)
• Consequence: MEGF9 NM_001080497.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973

Genes affected

MEGF9 (HGNC:3234): (multiple EGF like domains 9) Predicted to be involved in several processes, including animal organ morphogenesis; cell migration; and substrate adhesion-dependent cell spreading. Predicted to be integral component of membrane. Predicted to be active in basement 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=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEGF9	NM_001080497.3	c.601+8466G>A		intron_variant		ENST00000373930.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEGF9	ENST00000373930.4	c.601+8466G>A		intron_variant		2	NM_001080497.3	P1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88468 AN: 151358 Hom.: 28587 Cov.: 30

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.584 AC: 88478 AN: 151476 Hom.: 28594 Cov.: 30 AF XY: 0.591 AC XY: 43723 AN XY: 73994

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.614

Alfa AF: 0.677 Hom.: 19028

Bravo AF: 0.566

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	9.0
Dann	Benign	0.50

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: rs10760112; hg19: chr9-123467570;