Variant 7-6410163-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_139179.4(DAGLB):c.1787T>C(p.Ile596Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00805 in 1,580,808 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0070 ( 9 hom., cov: 32)

Exomes 𝑓: 0.0082 ( 78 hom. )

Consequence

DAGLB
NM_139179.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.11

Variant links:

Genes affected

DAGLB (HGNC:28923): (diacylglycerol lipase beta) Enables lipase activity. Involved in arachidonic acid metabolic process. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

DAGLB links:

DAGLB (HGNC:):

DAGLB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011635125).

BP6

Variant 7-6410163-A-G is Benign according to our data. Variant chr7-6410163-A-G is described in ClinVar as [Benign]. Clinvar id is 771156.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAGLB	NM_139179.4 linkuse as main transcript	c.1787T>C	p.Ile596Thr	missense_variant	14/15	ENST00000297056.11	NP_631918.3	Q8NCG7-1
DAGLB	NM_001142936.2 linkuse as main transcript	c.1400T>C	p.Ile467Thr	missense_variant	12/13		NP_001136408.1	Q8NCG7-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAGLB	ENST00000297056.11 linkuse as main transcript	c.1787T>C	p.Ile596Thr	missense_variant	14/15	1	NM_139179.4	ENSP00000297056.6		Q8NCG7-1

Frequencies

GnomAD3 genomes

AF:

0.00703

AC:

1069

AN:

152074

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00563

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.0156

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.00718

GnomAD3 exomes

AF:

0.00703

AC:

1508

AN:

214474

Hom.:

AF XY:

0.00698

AC XY:

807

AN XY:

115592

show subpopulations

Gnomad AFR exome

AF:

0.00126

Gnomad AMR exome

AF:

0.00364

Gnomad ASJ exome

AF:

0.00546

Gnomad EAS exome

AF:

0.0000595

Gnomad SAS exome

AF:

0.00194

Gnomad FIN exome

AF:

0.0180

Gnomad NFE exome

AF:

0.00946

Gnomad OTH exome

AF:

0.00863

GnomAD4 exome

AF:

0.00816

AC:

11663

AN:

1428616

Hom.:

Cov.:

AF XY:

0.00815

AC XY:

5757

AN XY:

706472

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00416

Gnomad4 ASJ exome

AF:

0.00465

Gnomad4 EAS exome

AF:

0.0000257

Gnomad4 SAS exome

AF:

0.00198

Gnomad4 FIN exome

AF:

0.0166

Gnomad4 NFE exome

AF:

0.00901

Gnomad4 OTH exome

AF:

0.00784

GnomAD4 genome

AF:

0.00702

AC:

1069

AN:

152192

Hom.:

Cov.:

AF XY:

0.00696

AC XY:

518

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.00164

Gnomad4 AMR

AF:

0.00563

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.0156

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.00711

Alfa

AF:

0.00969

Hom.:

Bravo

AF:

0.00553

TwinsUK

AF:

0.00701

AC:

ALSPAC

AF:

0.00778

AC:

ESP6500AA

AF:

0.000909

AC:

ESP6500EA

AF:

0.00803

AC:

ExAC

AF:

0.00631

AC:

765

Asia WGS

AF:

0.000289

AC:

AN:

3478

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

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.88

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Uncertain

0.030

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.43

T;.;T

Eigen

Uncertain

0.64

Eigen_PC

Uncertain

0.65

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.91

D;D;D

MetaRNN

Benign

0.012

T;T;T

MetaSVM

Uncertain

-0.19

MutationAssessor

Uncertain

2.8

M;.;.

PrimateAI

Uncertain

0.66

PROVEAN

Uncertain

-4.0

D;D;D

REVEL

Uncertain

0.48

Sift

Uncertain

0.0010

D;D;D

Sift4G

Uncertain

0.0030

D;D;D

Polyphen

1.0

D;.;.

Vest4

0.86

MVP

0.80

MPC

0.25

ClinPred

0.018

GERP RS

5.9

Varity_R

0.42

gMVP

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over