chr11-75798369-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032564.5(DGAT2):c.952G>A(p.Gly318Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00139 in 1,614,098 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0010 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 6 hom. )
Consequence
DGAT2
NM_032564.5 missense
NM_032564.5 missense
Scores
1
7
11
Clinical Significance
Conservation
PhyloP100: 5.88
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 -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.05042523).
BP6
?
Variant 11-75798369-G-A is Benign according to our data. Variant chr11-75798369-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2642164.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.952G>A | p.Gly318Ser | missense_variant | 7/8 | ENST00000228027.12 | |
DGAT2 | NM_001253891.2 | c.823G>A | p.Gly275Ser | missense_variant | 6/7 | ||
DGAT2 | XM_011545304.3 | c.862G>A | p.Gly288Ser | missense_variant | 7/8 | ||
DGAT2 | XM_047427716.1 | c.679G>A | p.Gly227Ser | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGAT2 | ENST00000228027.12 | c.952G>A | p.Gly318Ser | missense_variant | 7/8 | 1 | NM_032564.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00101 AC: 154AN: 152204Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000883 AC: 222AN: 251296Hom.: 0 AF XY: 0.000942 AC XY: 128AN XY: 135836
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GnomAD4 exome AF: 0.00143 AC: 2087AN: 1461776Hom.: 6 Cov.: 31 AF XY: 0.00136 AC XY: 990AN XY: 727190
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GnomAD4 genome ? AF: 0.00101 AC: 154AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000873 AC XY: 65AN XY: 74482
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | DGAT2: BS1 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;.
REVEL
Benign
Sift
Benign
D;T;.
Sift4G
Uncertain
D;D;D
Polyphen
P;P;.
Vest4
MVP
MPC
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