19-42375658-G-A

Position:

chr19-42375658-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001271938.2(MEGF8):c.7421G>A(p.Arg2474His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00493 in 1,610,068 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0051 ( 22 hom. )

Consequence

MEGF8
NM_001271938.2 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 7.40

Variant links:

Genes affected

MEGF8 (HGNC:3233): (multiple EGF like domains 8) The protein encoded by this gene is a single-pass type I membrane protein of unknown function that contains several EGF-like domains, Kelch repeats, and PSI domains. Defects in this gene are a cause of Carpenter syndrome 2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

MEGF8 links:

MEGF8 (HGNC:):

MEGF8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0077979267).

BP6

Variant 19-42375658-G-A is Benign according to our data. Variant chr19-42375658-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 473346.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-42375658-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00322 (490/152230) while in subpopulation SAS AF= 0.00642 (31/4828). AF 95% confidence interval is 0.00465. There are 2 homozygotes in gnomad4. There are 220 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEGF8	NM_001271938.2 linkuse as main transcript	c.7421G>A	p.Arg2474His	missense_variant	42/42	ENST00000251268.11	NP_001258867.1	Q7Z7M0-1
MEGF8	NM_001410.3 linkuse as main transcript	c.7220G>A	p.Arg2407His	missense_variant	41/41		NP_001401.2	Q7Z7M0-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEGF8	ENST00000251268.11 linkuse as main transcript	c.7421G>A	p.Arg2474His	missense_variant	42/42	5	NM_001271938.2	ENSP00000251268.5		Q7Z7M0-1

Frequencies

GnomAD3 genomes

AF:

0.00321

AC:

489

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00138

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00621

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.00491

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00395

AC:

959

AN:

242648

Hom.:

AF XY:

0.00417

AC XY:

550

AN XY:

131860

show subpopulations

Gnomad AFR exome

AF:

0.00100

Gnomad AMR exome

AF:

0.00363

Gnomad ASJ exome

AF:

0.00717

Gnomad EAS exome

AF:

0.0000555

Gnomad SAS exome

AF:

0.00551

Gnomad FIN exome

AF:

0.000236

Gnomad NFE exome

AF:

0.00505

Gnomad OTH exome

AF:

0.00503

GnomAD4 exome

AF:

0.00510

AC:

7442

AN:

1457838

Hom.:

Cov.:

AF XY:

0.00524

AC XY:

3800

AN XY:

724860

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.00398

Gnomad4 ASJ exome

AF:

0.00667

Gnomad4 EAS exome

AF:

0.0000758

Gnomad4 SAS exome

AF:

0.00528

Gnomad4 FIN exome

AF:

0.000342

Gnomad4 NFE exome

AF:

0.00561

Gnomad4 OTH exome

AF:

0.00518

GnomAD4 genome

AF:

0.00322

AC:

490

AN:

152230

Hom.:

Cov.:

AF XY:

0.00296

AC XY:

220

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00137

Gnomad4 AMR

AF:

0.00320

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00642

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00491

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00491

Hom.:

Bravo

AF:

0.00354

TwinsUK

AF:

0.00539

AC:

ALSPAC

AF:

0.00623

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00454

AC:

ExAC

AF:

0.00377

AC:

457

ClinVar

Significance: Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2024	MEGF8: BS2 -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

MEGF8-related Carpenter syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

MEGF8-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 24, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.28

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.11

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.20

.;.;T

Eigen

Uncertain

0.68

Eigen_PC

Pathogenic

0.68

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.91

D;D;D

M_CAP

Benign

0.028

MetaRNN

Benign

0.0078

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.4

.;.;M

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-2.3

N;D;N

REVEL

Benign

0.28

Sift

Uncertain

0.0080

D;D;D

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

1.0

D;D;D

Vest4

0.36

MVP

0.13

MPC

1.6

ClinPred

0.020

GERP RS

4.9

Varity_R

0.24

gMVP

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over