Variant chr7-101196248-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000223114.9(MOGAT3):c.810C>T(p.Arg270Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00354 in 1,603,188 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 20 hom. )

Consequence

MOGAT3
ENST00000223114.9 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -13.2

Variant links:

Genes affected

MOGAT3 (HGNC:23249): (monoacylglycerol O-acyltransferase 3) Acyl-CoA:monoacylglycerol acyltransferase (MOGAT; EC 2.3.1.22) catalyzes the synthesis of diacylglycerol from 2-monoacylglycerol and fatty acyl-CoA (Cheng et al., 2003 [PubMed 12618427]).[supplied by OMIM, Mar 2008]

MOGAT3 links:

MOGAT3 (HGNC:):

MOGAT3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 7-101196248-G-A is Benign according to our data. Variant chr7-101196248-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657855.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-13.2 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOGAT3	NM_178176.4 linkuse as main transcript	c.810C>T	p.Arg270Arg	synonymous_variant	6/7	ENST00000223114.9	NP_835470.1	Q86VF5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MOGAT3	ENST00000223114.9 linkuse as main transcript	c.810C>T	p.Arg270Arg	synonymous_variant	6/7	1	NM_178176.4	ENSP00000223114.4	Q86VF5-1
MOGAT3	ENST00000379423.3 linkuse as main transcript	c.669-148C>T		intron_variant		1		ENSP00000368734.3	Q86VF5-2
MOGAT3	ENST00000440203.6 linkuse as main transcript	c.810C>T	p.Arg270Arg	synonymous_variant	6/6	2		ENSP00000403756.2	Q86VF5-3

Frequencies

GnomAD3 genomes

AF:

0.00214

AC:

326

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000458

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.000654

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00332

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00363

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00251

AC:

573

AN:

228500

Hom.:

AF XY:

0.00246

AC XY:

304

AN XY:

123534

show subpopulations

Gnomad AFR exome

AF:

0.000281

Gnomad AMR exome

AF:

0.00122

Gnomad ASJ exome

AF:

0.00598

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00315

Gnomad FIN exome

AF:

0.000757

Gnomad NFE exome

AF:

0.00347

Gnomad OTH exome

AF:

0.00261

GnomAD4 exome

AF:

0.00369

AC:

5349

AN:

1450884

Hom.:

Cov.:

AF XY:

0.00370

AC XY:

2664

AN XY:

720578

show subpopulations

Gnomad4 AFR exome

AF:

0.000810

Gnomad4 AMR exome

AF:

0.00127

Gnomad4 ASJ exome

AF:

0.00558

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00298

Gnomad4 FIN exome

AF:

0.000531

Gnomad4 NFE exome

AF:

0.00410

Gnomad4 OTH exome

AF:

0.00455

GnomAD4 genome

AF:

0.00213

AC:

325

AN:

152304

Hom.:

Cov.:

AF XY:

0.00176

AC XY:

131

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.000457

Gnomad4 AMR

AF:

0.000653

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00311

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00363

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00322

Hom.:

Bravo

AF:

0.00212

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

MOGAT3: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.90

DANN

Benign

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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