rs3841596

chr11-75798591-GGTA-Gchr11-75798591-GGTA-GGTAGTA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_032564.5(DGAT2):c.1012+170_1012+172del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,170 control chromosomes in the GnomAD database, including 935 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (935 hom., cov: 31)
• Consequence: DGAT2 NM_032564.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

Genes affected

DGAT2 (HGNC:16940): (diacylglycerol O-acyltransferase 2) This gene encodes one of two enzymes which catalyzes the final reaction in the synthesis of triglycerides in which diacylglycerol is covalently bound to long chain fatty acyl-CoAs. The encoded protein catalyzes this reaction at low concentrations of magnesium chloride while the other enzyme has high activity at high concentrations of magnesium chloride. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGAT2	NM_032564.5	c.1012+170_1012+172del		intron_variant		ENST00000228027.12
DGAT2	NM_001253891.2	c.883+170_883+172del		intron_variant
DGAT2	XM_011545304.3	c.922+170_922+172del		intron_variant
DGAT2	XM_047427716.1	c.739+170_739+172del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGAT2	ENST00000228027.12	c.1012+170_1012+172del		intron_variant		1	NM_032564.5	P1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16365 AN: 152052 Hom.: 937 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0993

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

GnomAD4 genome AF: 0.108 AC: 16372 AN: 152170 Hom.: 935 Cov.: 31 AF XY: 0.106 AC XY: 7860 AN XY: 74382

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.0731

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.101

Alfa AF: 0.111 Hom.: 111

Bravo AF: 0.111

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3841596; hg19: chr11-75509636;