chr11-75797213-T-C
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_032564.5(DGAT2):c.690T>C(p.Ser230=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00712 in 1,572,188 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0047 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0074 ( 49 hom. )
Consequence
DGAT2
NM_032564.5 synonymous
NM_032564.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.03
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 11-75797213-T-C is Benign according to our data. Variant chr11-75797213-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 708403.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-75797213-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-2.03 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGAT2 | NM_032564.5 | c.690T>C | p.Ser230= | synonymous_variant | 6/8 | ENST00000228027.12 | |
DGAT2 | NM_001253891.2 | c.561T>C | p.Ser187= | synonymous_variant | 5/7 | ||
DGAT2 | XM_011545304.3 | c.600T>C | p.Ser200= | synonymous_variant | 6/8 | ||
DGAT2 | XM_047427716.1 | c.417T>C | p.Ser139= | synonymous_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGAT2 | ENST00000228027.12 | c.690T>C | p.Ser230= | synonymous_variant | 6/8 | 1 | NM_032564.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00470 AC: 715AN: 152000Hom.: 6 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
715
AN:
152000
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00456 AC: 996AN: 218378Hom.: 5 AF XY: 0.00481 AC XY: 570AN XY: 118480
GnomAD3 exomes
AF:
AC:
996
AN:
218378
Hom.:
AF XY:
AC XY:
570
AN XY:
118480
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00738 AC: 10475AN: 1420070Hom.: 49 Cov.: 30 AF XY: 0.00735 AC XY: 5186AN XY: 705212
GnomAD4 exome
AF:
AC:
10475
AN:
1420070
Hom.:
Cov.:
30
AF XY:
AC XY:
5186
AN XY:
705212
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00470 AC: 715AN: 152118Hom.: 6 Cov.: 32 AF XY: 0.00457 AC XY: 340AN XY: 74380
GnomAD4 genome
?
AF:
AC:
715
AN:
152118
Hom.:
Cov.:
32
AF XY:
AC XY:
340
AN XY:
74380
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
13
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | DGAT2: BP4, BP7, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at