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GeneBe

X-70204458-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_198512.3(DGAT2L6):c.801G>T(p.Arg267=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000901 in 1,209,535 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 39 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00048 ( 0 hom., 22 hem., cov: 22)
Exomes 𝑓: 0.000051 ( 0 hom. 17 hem. )

Consequence

DGAT2L6
NM_198512.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.41
Variant links:
Genes affected
DGAT2L6 (HGNC:23250): (diacylglycerol O-acyltransferase 2 like 6) This gene is a member of the diacylglycerol acyltransferase 2 family. The encoded protein is a putative acyltransferase and is most likely involved in the synthesis of di- or triacylglycerol, however its substrate specificity is currently unknown. [provided by RefSeq, Feb 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-70204458-G-T is Benign according to our data. Variant chrX-70204458-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3042676.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.41 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAd at 22 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DGAT2L6NM_198512.3 linkuse as main transcriptc.801G>T p.Arg267= synonymous_variant 6/7 ENST00000333026.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DGAT2L6ENST00000333026.4 linkuse as main transcriptc.801G>T p.Arg267= synonymous_variant 6/71 NM_198512.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000475
AC:
53
AN:
111487
Hom.:
0
Cov.:
22
AF XY:
0.000654
AC XY:
22
AN XY:
33659
show subpopulations
Gnomad AFR
AF:
0.00134
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000856
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000283
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00133
GnomAD3 exomes
AF:
0.000153
AC:
28
AN:
183372
Hom.:
0
AF XY:
0.000147
AC XY:
10
AN XY:
67838
show subpopulations
Gnomad AFR exome
AF:
0.00190
Gnomad AMR exome
AF:
0.000109
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000510
AC:
56
AN:
1097995
Hom.:
0
Cov.:
31
AF XY:
0.0000468
AC XY:
17
AN XY:
363409
show subpopulations
Gnomad4 AFR exome
AF:
0.00167
Gnomad4 AMR exome
AF:
0.000114
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:
0.00000119
Gnomad4 OTH exome
AF:
0.000152
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000475
AC:
53
AN:
111540
Hom.:
0
Cov.:
22
AF XY:
0.000652
AC XY:
22
AN XY:
33722
show subpopulations
Gnomad4 AFR
AF:
0.00133
Gnomad4 AMR
AF:
0.000855
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000284
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00131
Alfa
AF:
0.0000398
Hom.:
0
Bravo
AF:
0.000703

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

DGAT2L6-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJul 10, 2019This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
0.42
Dann
Benign
0.37

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs140170619; hg19: chrX-69424308; API