NM_012079.6:c.579C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_012079.6(DGAT1):c.579C>T(p.Gly193Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 1,610,914 control chromosomes in the GnomAD database, including 3,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 232 hom., cov: 33)

Exomes 𝑓: 0.065 ( 3434 hom. )

Consequence

DGAT1
NM_012079.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.158

Publications

8 publications found

Variant links:

Genes affected

DGAT1 (HGNC:2843): (diacylglycerol O-acyltransferase 1) This gene encodes an multipass transmembrane protein that functions as a key metabolic enzyme. The encoded protein catalyzes the conversion of diacylglycerol and fatty acyl CoA to triacylglycerol. This enzyme can also transfer acyl CoA to retinol. Activity of this protein may be associated with obesity and other metabolic diseases. [provided by RefSeq, Jul 2013]

DGAT1 Gene-Disease associations (from GenCC):

congenital diarrhea 7 with exudative enteropathy
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, PanelApp Australia, Ambry Genetics

DGAT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 8-144318358-G-A is Benign according to our data. Variant chr8-144318358-G-A is described in ClinVar as Benign. ClinVar VariationId is 402588.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.158 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012079.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGAT1	NM_012079.6	MANE Select	c.579C>T	p.Gly193Gly	synonymous	Exon 7 of 17	NP_036211.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
DGAT1	ENST00000528718.6	TSL:1 MANE Select	c.579C>T	p.Gly193Gly	synonymous	Exon 7 of 17	ENSP00000482264.1
DGAT1	ENST00000332324.5	TSL:5	c.579C>T	p.Gly193Gly	synonymous	Exon 7 of 10	ENSP00000332258.5
DGAT1	ENST00000524965.5	TSL:5	n.137C>T		non_coding_transcript_exon	Exon 3 of 12

Frequencies

GnomAD3 genomes

AF:

0.0462

AC:

7034

AN:

152204

Hom.:

232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0141

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0501

Gnomad ASJ

AF:

0.0397

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0105

Gnomad FIN

AF:

0.0473

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0710

Gnomad OTH

AF:

0.0669

GnomAD2 exomes

AF:

0.0474

AC:

11711

AN:

246882

AF XY:

0.0482

show subpopulations

Gnomad AFR exome

AF:

0.0104

Gnomad AMR exome

AF:

0.0371

Gnomad ASJ exome

AF:

0.0457

Gnomad EAS exome

AF:

0.0000546

Gnomad FIN exome

AF:

0.0460

Gnomad NFE exome

AF:

0.0733

Gnomad OTH exome

AF:

0.0535

GnomAD4 exome

AF:

0.0649

AC:

94590

AN:

1458592

Hom.:

3434

Cov.:

AF XY:

0.0636

AC XY:

46112

AN XY:

725412

show subpopulations

African (AFR)

AF:

0.0107

AC:

358

AN:

33460

American (AMR)

AF:

0.0387

AC:

1723

AN:

44566

Ashkenazi Jewish (ASJ)

AF:

0.0448

AC:

1165

AN:

26000

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39660

South Asian (SAS)

AF:

0.0129

AC:

1111

AN:

86086

European-Finnish (FIN)

AF:

0.0469

AC:

2447

AN:

52184

Middle Eastern (MID)

AF:

0.0337

AC:

194

AN:

5758

European-Non Finnish (NFE)

AF:

0.0757

AC:

84113

AN:

1110590

Other (OTH)

AF:

0.0577

AC:

3478

AN:

60288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

4379

8757

13136

17514

21893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3030

6060

9090

12120

15150

<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:

0.0462

AC:

7032

AN:

152322

Hom.:

232

Cov.:

AF XY:

0.0442

AC XY:

3293

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.0140

AC:

583

AN:

41574

American (AMR)

AF:

0.0500

AC:

766

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0397

AC:

138

AN:

3472

East Asian (EAS)

AF:

0.000772

AC:

AN:

5178

South Asian (SAS)

AF:

0.0106

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.0473

AC:

502

AN:

10618

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0710

AC:

4826

AN:

68018

Other (OTH)

AF:

0.0667

AC:

141

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

351

702

1052

1403

1754

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0597

Hom.:

253

Bravo

AF:

0.0459

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Jun 09, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

7.4

(source)

DANN

Benign

0.76

PhyloP100

-0.16

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over