rs1017713

Positions:

• chr11-75788407-T-C

Variant summary

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

The NM_032564.5(DGAT2):​c.251-1781T>C 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 152,270 control chromosomes in the GnomAD database, including 965 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 0.11 (965 hom., cov: 32)
• Consequence: DGAT2 NM_032564.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGAT2	NM_032564.5	c.251-1781T>C		intron_variant		ENST00000228027.12
DGAT2	NM_001253891.2	c.122-1781T>C		intron_variant
DGAT2	XM_011545304.3	c.161-1781T>C		intron_variant
DGAT2	XM_047427716.1	c.-23-1781T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGAT2	ENST00000228027.12	c.251-1781T>C		intron_variant		1	NM_032564.5	P1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16492 AN: 152152 Hom.: 967 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0961

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.108 AC: 16500 AN: 152270 Hom.: 965 Cov.: 32 AF XY: 0.106 AC XY: 7928 AN XY: 74458

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0962

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0961

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0965 Hom.: 761

Bravo AF: 0.111

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.64

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: rs1017713; hg19: chr11-75499452;