Variant 11-61720218-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_006133.3(DAGLA):c.63G>A(p.Pro21Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,613,452 control chromosomes in the GnomAD database, including 56,857 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.25 ( 5152 hom., cov: 33)

Exomes 𝑓: 0.26 ( 51705 hom. )

Consequence

DAGLA
NM_006133.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.75

Variant links:

Genes affected

DAGLA (HGNC:1165): (diacylglycerol lipase alpha) This gene encodes a diacylglycerol lipase. The encoded enzyme is involved in the biosynthesis of the endocannabinoid 2-arachidonoyl-glycerol.[provided by RefSeq, Nov 2010]

DAGLA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 11-61720218-G-A is Benign according to our data. Variant chr11-61720218-G-A is described in ClinVar as [Benign]. Clinvar id is 3060353.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.75 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAGLA	NM_006133.3 linkuse as main transcript	c.63G>A	p.Pro21Pro	synonymous_variant	2/20	ENST00000257215.10	NP_006124.1	Q9Y4D2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAGLA	ENST00000257215.10 linkuse as main transcript	c.63G>A	p.Pro21Pro	synonymous_variant	2/20	1	NM_006133.3	ENSP00000257215.5		Q9Y4D2
DAGLA	ENST00000540717.1 linkuse as main transcript	n.63G>A		non_coding_transcript_exon_variant	2/20	5		ENSP00000440264.1		F5GY58

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38631

AN:

152012

Hom.:

5155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.274

AC:

68888

AN:

251166

Hom.:

9949

AF XY:

0.272

AC XY:

36998

AN XY:

135798

show subpopulations

Gnomad AFR exome

AF:

0.216

Gnomad AMR exome

AF:

0.305

Gnomad ASJ exome

AF:

0.225

Gnomad EAS exome

AF:

0.460

Gnomad SAS exome

AF:

0.260

Gnomad FIN exome

AF:

0.252

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.267

GnomAD4 exome

AF:

0.263

AC:

383873

AN:

1461322

Hom.:

51705

Cov.:

AF XY:

0.262

AC XY:

190421

AN XY:

727026

show subpopulations

Gnomad4 AFR exome

AF:

0.213

Gnomad4 AMR exome

AF:

0.305

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.388

Gnomad4 SAS exome

AF:

0.259

Gnomad4 FIN exome

AF:

0.251

Gnomad4 NFE exome

AF:

0.259

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.254

AC:

38631

AN:

152130

Hom.:

5152

Cov.:

AF XY:

0.256

AC XY:

19012

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.272

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.252

Gnomad4 OTH

AF:

0.261

Alfa

AF:

0.252

Hom.:

6704

Bravo

AF:

0.256

Asia WGS

AF:

0.327

AC:

1137

AN:

3478

EpiCase

AF:

0.253

EpiControl

AF:

0.256

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DAGLA-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as 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

-0.42

CADD

Benign

0.73

DANN

Benign

0.85

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.

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