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GeneBe

11-75798272-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PM4BP6_Moderate

The NM_032564.5(DGAT2):c.855C>A(p.Tyr285Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000596 in 1,614,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00051 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00061 ( 0 hom. )

Consequence

DGAT2
NM_032564.5 stop_gained

Scores

2
4
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.18
Variant links:
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Stoplost variant in NM_032564.5 Downstream stopcodon found after 459 codons.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-75798272-C-A is Benign according to our data. Variant chr11-75798272-C-A is described in ClinVar as [Benign]. Clinvar id is 2642162.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DGAT2NM_032564.5 linkuse as main transcriptc.855C>A p.Tyr285Ter stop_gained 7/8 ENST00000228027.12
DGAT2NM_001253891.2 linkuse as main transcriptc.726C>A p.Tyr242Ter stop_gained 6/7
DGAT2XM_011545304.3 linkuse as main transcriptc.765C>A p.Tyr255Ter stop_gained 7/8
DGAT2XM_047427716.1 linkuse as main transcriptc.582C>A p.Tyr194Ter stop_gained 7/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DGAT2ENST00000228027.12 linkuse as main transcriptc.855C>A p.Tyr285Ter stop_gained 7/81 NM_032564.5 P1Q96PD7-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000506
AC:
77
AN:
152192
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000867
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.000509
AC:
128
AN:
251442
Hom.:
0
AF XY:
0.000478
AC XY:
65
AN XY:
135894
show subpopulations
Gnomad AFR exome
AF:
0.000246
Gnomad AMR exome
AF:
0.000260
Gnomad ASJ exome
AF:
0.000198
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.0000924
Gnomad NFE exome
AF:
0.000914
Gnomad OTH exome
AF:
0.000978
GnomAD4 exome
AF:
0.000605
AC:
885
AN:
1461880
Hom.:
0
Cov.:
31
AF XY:
0.000572
AC XY:
416
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
Gnomad4 AMR exome
AF:
0.000425
Gnomad4 ASJ exome
AF:
0.000191
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.0000936
Gnomad4 NFE exome
AF:
0.000730
Gnomad4 OTH exome
AF:
0.000563
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000506
AC:
77
AN:
152310
Hom.:
0
Cov.:
32
AF XY:
0.000443
AC XY:
33
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.000653
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000867
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000675
Hom.:
0
Bravo
AF:
0.000555
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000582
AC:
5
ExAC
?
    Exome Aggregation Consortium database
AF:
0.000626
AC:
76
EpiCase
AF:
0.000709
EpiControl
AF:
0.000948

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2022DGAT2: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.30
D
BayesDel_noAF
Pathogenic
0.59
Cadd
Pathogenic
36
Dann
Uncertain
1.0
Eigen
Uncertain
0.41
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Uncertain
0.91
D
MutationTaster
Benign
1.0
A;A
Vest4
0.93
GERP RS
2.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs150303834; hg19: chr11-75509317; API