Variant rs56180335 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_012079.6(DGAT1):c.579C>T(p.Gly193=) 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

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGAT1	NM_012079.6 linkuse as main transcript	c.579C>T	p.Gly193=	synonymous_variant	7/17	ENST00000528718.6	NP_036211.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGAT1	ENST00000528718.6 linkuse as main transcript	c.579C>T	p.Gly193=	synonymous_variant	7/17	1	NM_012079.6	ENSP00000482264	P1

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

GnomAD3 exomes

AF:

0.0474

AC:

11711

AN:

246882

Hom.:

382

AF XY:

0.0482

AC XY:

6465

AN XY:

134132

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 SAS exome

AF:

0.0128

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

Gnomad4 AFR exome

AF:

0.0107

Gnomad4 AMR exome

AF:

0.0387

Gnomad4 ASJ exome

AF:

0.0448

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0129

Gnomad4 FIN exome

AF:

0.0469

Gnomad4 NFE exome

AF:

0.0757

Gnomad4 OTH exome

AF:

0.0577

GnomAD4 genome

AF:

0.0462

AC:

7032

AN:

152322

Hom.:

232

Cov.:

AF XY:

0.0442

AC XY:

3293

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0140

Gnomad4 AMR

AF:

0.0500

Gnomad4 ASJ

AF:

0.0397

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0106

Gnomad4 FIN

AF:

0.0473

Gnomad4 NFE

AF:

0.0710

Gnomad4 OTH

AF:

0.0667

Alfa

AF:

0.0616

Hom.:

197

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

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

7.4

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over