rs1944438

Positions:

• chr11-75772578-A-G
• chr11-75772578-A-T

Variant summary

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

The NM_032564.5(DGAT2):​c.121+3466A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,030 control chromosomes in the GnomAD database, including 14,622 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 0.40 (14622 hom., cov: 32)
• Consequence: DGAT2 NM_032564.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGAT2	NM_032564.5	c.121+3466A>G		intron_variant		ENST00000228027.12
DGAT2	XM_047427716.1	c.-1392A>G		5_prime_UTR_variant	1/8
DGAT2	NM_001253891.2	c.121+3466A>G		intron_variant
DGAT2	XM_011545304.3	c.31+1456A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGAT2	ENST00000228027.12	c.121+3466A>G		intron_variant		1	NM_032564.5	P1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60701 AN: 151912 Hom.: 14621 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.399 AC: 60713 AN: 152030 Hom.: 14622 Cov.: 32 AF XY: 0.398 AC XY: 29562 AN XY: 74308

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.467

Alfa AF: 0.498 Hom.: 7828

Bravo AF: 0.382

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.22

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: rs1944438; hg19: chr11-75483623;