rs7003945

Variant names:

• chr8-144326802-G-A
• rs7003945
• NM_012079.6:c.-166C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-144326802-G-A
• chr8-144326802-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012079.6(DGAT1):​c.-166C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 434,950 control chromosomes in the GnomAD database, including 47,421 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 0.39 (13318 hom., cov: 34)
  • Exomes 𝑓: 0.49 (34103 hom.)
• Consequence: DGAT1 NM_012079.6 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.69

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGAT1	NM_012079.6	c.-166C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 17	ENST00000528718.6	NP_036211.2
DGAT1	NM_012079.6	c.-166C>T		5_prime_UTR_variant	Exon 1 of 17	ENST00000528718.6	NP_036211.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGAT1	ENST00000528718.6	c.-166C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 17	1	NM_012079.6	ENSP00000482264.1
DGAT1	ENST00000528718.6	c.-166C>T		5_prime_UTR_variant	Exon 1 of 17	1	NM_012079.6	ENSP00000482264.1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59767 AN: 151966 Hom.: 13318 Cov.: 34

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.399

GnomAD4 exome AF: 0.485 AC: 137215 AN: 282876 Hom.: 34103 Cov.: 5 AF XY: 0.485 AC XY: 67612 AN XY: 139280

Gnomad4 AFR exome AF: 0.162 AC: 942 AN: 5826

Gnomad4 AMR exome AF: 0.306 AC: 855 AN: 2792

Gnomad4 ASJ exome AF: 0.512 AC: 1887 AN: 3686

Gnomad4 EAS exome AF: 0.482 AC: 3053 AN: 6328

Gnomad4 SAS exome AF: 0.344 AC: 1716 AN: 4992

Gnomad4 FIN exome AF: 0.471 AC: 4557 AN: 9678

Gnomad4 NFE exome AF: 0.500 AC: 118413 AN: 236794

Gnomad4 Remaining exome AF: 0.455 AC: 5451 AN: 11982

GnomAD4 genome AF: 0.393 AC: 59766 AN: 152074 Hom.: 13318 Cov.: 34 AF XY: 0.389 AC XY: 28922 AN XY: 74352

Gnomad4 AFR AF: 0.188 AC: 0.188238 AN: 0.188238

Gnomad4 AMR AF: 0.324 AC: 0.323829 AN: 0.323829

Gnomad4 ASJ AF: 0.513 AC: 0.512687 AN: 0.512687

Gnomad4 EAS AF: 0.522 AC: 0.522304 AN: 0.522304

Gnomad4 SAS AF: 0.347 AC: 0.346935 AN: 0.346935

Gnomad4 FIN AF: 0.458 AC: 0.458499 AN: 0.458499

Gnomad4 NFE AF: 0.507 AC: 0.506652 AN: 0.506652

Gnomad4 OTH AF: 0.400 AC: 0.40019 AN: 0.40019

Alfa AF: 0.302 Hom.: 855

Bravo AF: 0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.92
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7003945; hg19: chr8-145550465;