chr2-222702297-A-G

Position:

• chr2-222702297-A-G

Variant summary

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

The NM_058165.3(MOGAT1):​c.853+7009A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,904 control chromosomes in the GnomAD database, including 18,725 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 0.49 (18725 hom., cov: 32)
• Consequence: MOGAT1 NM_058165.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

Genes affected

MOGAT1 (HGNC:18210): (monoacylglycerol O-acyltransferase 1) Acyl-CoA:monoacylglycerol acyltransferase (MOGAT; EC 2.3.1.22) catalyzes the synthesis of diacylglycerols, the precursor of physiologically important lipids such as triacylglycerol and phospholipids (Yen et al., 2002 [PubMed 12077311]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOGAT1	NM_058165.3	c.853+7009A>G		intron_variant		ENST00000446656.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOGAT1	ENST00000446656.4	c.853+7009A>G		intron_variant		5	NM_058165.3	P1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74006 AN: 151784 Hom.: 18713 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.487 AC: 74045 AN: 151904 Hom.: 18725 Cov.: 32 AF XY: 0.480 AC XY: 35611 AN XY: 74244

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.522

Alfa AF: 0.540 Hom.: 44474

Bravo AF: 0.498

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
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: rs951997; hg19: chr2-223567016;