Genetic Variant DGAT2:c.*19T>C (chr11-75800527-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_032564.5(DGAT2):c.*19T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,611,350 control chromosomes in the GnomAD database, including 17,817 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.21 ( 5491 hom., cov: 33)

Exomes 𝑓: 0.11 ( 12326 hom. )

Consequence

DGAT2
NM_032564.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.677

Variant links:

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]

DGAT2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 11-75800527-T-C is Benign according to our data. Variant chr11-75800527-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
DGAT2	NM_032564.5 link	c.*19T>C	3_prime_UTR_variant	Exon 8 of 8	ENST00000228027.12	NP_115953.2	Q96PD7-1
DGAT2	NM_001253891.2 link	c.*19T>C	3_prime_UTR_variant	Exon 7 of 7		NP_001240820.1	Q96PD7-2
DGAT2	XM_011545304.3 link	c.*19T>C	3_prime_UTR_variant	Exon 8 of 8		XP_011543606.1
DGAT2	XM_047427716.1 link	c.*19T>C	3_prime_UTR_variant	Exon 8 of 8		XP_047283672.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGAT2	ENST00000228027.12 link	c.*19T>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_032564.5	ENSP00000228027.6		Q96PD7-1

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32110

AN:

152102

Hom.:

5471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.469

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.265

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.0778

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0984

Gnomad OTH

AF:

0.176

GnomAD2 exomes

AF:

0.140

AC:

34340

AN:

245940

AF XY:

0.132

show subpopulations

Gnomad AFR exome

AF:

0.479

Gnomad AMR exome

AF:

0.116

Gnomad ASJ exome

AF:

0.117

Gnomad EAS exome

AF:

0.268

Gnomad FIN exome

AF:

0.0874

Gnomad NFE exome

AF:

0.0946

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.109

AC:

159181

AN:

1459130

Hom.:

12326

Cov.:

AF XY:

0.108

AC XY:

78594

AN XY:

725666

show subpopulations

Gnomad4 AFR exome

AF:

0.481

AC:

16077

AN:

33408

Gnomad4 AMR exome

AF:

0.116

AC:

5145

AN:

44292

Gnomad4 ASJ exome

AF:

0.116

AC:

3010

AN:

26036

Gnomad4 EAS exome

AF:

0.292

AC:

11576

AN:

39614

Gnomad4 SAS exome

AF:

0.125

AC:

10699

AN:

85814

Gnomad4 FIN exome

AF:

0.0875

AC:

4659

AN:

53256

Gnomad4 NFE exome

AF:

0.0894

AC:

99309

AN:

1110674

Gnomad4 Remaining exome

AF:

0.133

AC:

8037

AN:

60282

Heterozygous variant carriers

6763

13525

20288

27050

33813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

3880

7760

11640

15520

19400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.211

AC:

32180

AN:

152220

Hom.:

5491

Cov.:

AF XY:

0.207

AC XY:

15426

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.470

AC:

0.469545

AN:

0.469545

Gnomad4 AMR

AF:

0.142

AC:

0.141615

AN:

0.141615

Gnomad4 ASJ

AF:

0.117

AC:

0.116715

AN:

0.116715

Gnomad4 EAS

AF:

0.266

AC:

0.266126

AN:

0.266126

Gnomad4 SAS

AF:

0.129

AC:

0.128992

AN:

0.128992

Gnomad4 FIN

AF:

0.0778

AC:

0.0777862

AN:

0.0777862

Gnomad4 NFE

AF:

0.0984

AC:

0.0983857

AN:

0.0983857

Gnomad4 OTH

AF:

0.177

AC:

0.177389

AN:

0.177389

Heterozygous variant carriers

1125

2249

3374

4498

5623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

302

604

906

1208

1510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.133

Hom.:

6811

Bravo

AF:

0.226

Asia WGS

AF:

0.252

AC:

876

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.92

DANN

Benign

0.44

Mutation Taster

=100/0

polymorphism (auto)

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over