chr11-75796353-C-G

Variant names:

• chr11-75796353-C-G
• NM_032564.5:c.455C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_032564.5(DGAT2):​c.455C>G​(p.Thr152Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: DGAT2 NM_032564.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.43

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3948214).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGAT2	NM_032564.5	c.455C>G	p.Thr152Ser	missense_variant	Exon 5 of 8	ENST00000228027.12	NP_115953.2
DGAT2	NM_001253891.2	c.326C>G	p.Thr109Ser	missense_variant	Exon 4 of 7		NP_001240820.1
DGAT2	XM_011545304.3	c.365C>G	p.Thr122Ser	missense_variant	Exon 5 of 8		XP_011543606.1
DGAT2	XM_047427716.1	c.182C>G	p.Thr61Ser	missense_variant	Exon 5 of 8		XP_047283672.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGAT2	ENST00000228027.12	c.455C>G	p.Thr152Ser	missense_variant	Exon 5 of 8	1	NM_032564.5	ENSP00000228027.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461786 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 727184

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.049	.;.;T;.;.;.
Eigen	Benign	0.043
Eigen_PC	Benign	0.18
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.93	D;D;D;T;T;D
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.39	T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.59	.;.;N;.;.;.
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-0.26	.;.;N;N;.;.
REVEL	Benign	0.12
Sift	Uncertain	0.023	.;.;D;D;.;.
Sift4G	Uncertain	0.059	T;D;D;D;T;D
Polyphen		0.80, 0.34	.;.;P;B;.;.
Vest4		0.30, 0.33
MutPred		0.60		.;.;Loss of glycosylation at T153 (P = 0.1262);.;.;.;
MVP		0.51
MPC		0.13
ClinPred		0.89	D
GERP RS		4.1
Varity_R		0.14
gMVP		0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-75507398;