chr11-75797272-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_032564.5(DGAT2):c.749G>A(p.Gly250Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,574,470 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 2 hom. )
Consequence
DGAT2
NM_032564.5 missense
NM_032564.5 missense
Scores
3
5
6
Clinical Significance
Conservation
PhyloP100: 9.49
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.068149924).
BP6
?
Variant 11-75797272-G-A is Benign according to our data. Variant chr11-75797272-G-A is described in ClinVar as [Benign]. Clinvar id is 2642161.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGAT2 | NM_032564.5 | c.749G>A | p.Gly250Asp | missense_variant | 6/8 | ENST00000228027.12 | |
DGAT2 | NM_001253891.2 | c.620G>A | p.Gly207Asp | missense_variant | 5/7 | ||
DGAT2 | XM_011545304.3 | c.659G>A | p.Gly220Asp | missense_variant | 6/8 | ||
DGAT2 | XM_047427716.1 | c.476G>A | p.Gly159Asp | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGAT2 | ENST00000228027.12 | c.749G>A | p.Gly250Asp | missense_variant | 6/8 | 1 | NM_032564.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00114 AC: 173AN: 152178Hom.: 1 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00115 AC: 250AN: 216904Hom.: 0 AF XY: 0.00111 AC XY: 131AN XY: 117740
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GnomAD4 exome AF: 0.00140 AC: 1985AN: 1422174Hom.: 2 Cov.: 30 AF XY: 0.00140 AC XY: 987AN XY: 706590
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GnomAD4 genome ? AF: 0.00114 AC: 173AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | DGAT2: BS1, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Pathogenic
D;D;D;D
Polyphen
1.0
.;D;D;.
Vest4
0.91, 0.89
MVP
MPC
0.64
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at