rs56180335

Variant names:

• chr8-144318358-G-A
• rs56180335
• NM_012079.6:c.579C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-144318358-G-A
• chr8-144318358-G-C

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.158

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]

ACMG classification

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 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 rank	MANE	Protein	UniProt
DGAT1	NM_012079.6	c.579C>T	p.Gly193Gly	synonymous_variant	Exon 7 of 17	ENST00000528718.6	NP_036211.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGAT1	ENST00000528718.6	c.579C>T	p.Gly193Gly	synonymous_variant	Exon 7 of 17	1	NM_012079.6	ENSP00000482264.1

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 7034 AN: 152204 Hom.: 232 Cov.: 33

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

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.: 34 AF XY: 0.0636 AC XY: 46112 AN XY: 725412

Gnomad4 AFR exome AF: 0.0107 AC: 358 AN: 33460

Gnomad4 AMR exome AF: 0.0387 AC: 1723 AN: 44566

Gnomad4 ASJ exome AF: 0.0448 AC: 1165 AN: 26000

Gnomad4 EAS exome AF: 0.0000252 AC: 1 AN: 39660

Gnomad4 SAS exome AF: 0.0129 AC: 1111 AN: 86086

Gnomad4 FIN exome AF: 0.0469 AC: 2447 AN: 52184

Gnomad4 NFE exome AF: 0.0757 AC: 84113 AN: 1110590

Gnomad4 Remaining exome AF: 0.0577 AC: 3478 AN: 60288

GnomAD4 genome AF: 0.0462 AC: 7032 AN: 152322 Hom.: 232 Cov.: 33 AF XY: 0.0442 AC XY: 3293 AN XY: 74478

Gnomad4 AFR AF: 0.0140 AC: 0.0140232 AN: 0.0140232

Gnomad4 AMR AF: 0.0500 AC: 0.0500392 AN: 0.0500392

Gnomad4 ASJ AF: 0.0397 AC: 0.0397465 AN: 0.0397465

Gnomad4 EAS AF: 0.000772 AC: 0.000772499 AN: 0.000772499

Gnomad4 SAS AF: 0.0106 AC: 0.0105503 AN: 0.0105503

Gnomad4 FIN AF: 0.0473 AC: 0.0472782 AN: 0.0472782

Gnomad4 NFE AF: 0.0710 AC: 0.0709518 AN: 0.0709518

Gnomad4 OTH AF: 0.0667 AC: 0.0666982 AN: 0.0666982

Alfa AF: 0.0597 Hom.: 253

Bravo AF: 0.0459

Asia WGS AF: 0.00606 AC: 23 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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 v4.3

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
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs56180335; hg19: chr8-145542021; COSMIC: COSV107403783; COSMIC: COSV107403783;