2-222702307-C-T

Variant names:

• chr2-222702307-C-T
• rs1374536
• NM_058165.3:c.853+7019C>T

Variant summary

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

The NM_058165.3(MOGAT1):​c.853+7019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,792 control chromosomes in the GnomAD database, including 33,245 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 0.64 (33245 hom., cov: 32)
• Consequence: MOGAT1 NM_058165.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOGAT1	NM_058165.3	c.853+7019C>T		intron_variant	Intron 5 of 5	ENST00000446656.4	NP_477513.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOGAT1	ENST00000446656.4	c.853+7019C>T		intron_variant	Intron 5 of 5	5	NM_058165.3	ENSP00000406674.3

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97749 AN: 151672 Hom.: 33190 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.645 AC: 97865 AN: 151792 Hom.: 33245 Cov.: 32 AF XY: 0.632 AC XY: 46851 AN XY: 74140

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.658

Alfa AF: 0.623 Hom.: 11528

Bravo AF: 0.671

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.037
DANN	Benign	0.43

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: rs1374536; hg19: chr2-223567026;