Variant chr11-61723014-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000257215.10(DAGLA):c.409+54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 1,378,648 control chromosomes in the GnomAD database, including 67,289 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.24 ( 5456 hom., cov: 33)

Exomes 𝑓: 0.30 ( 61833 hom. )

Consequence

DAGLA
ENST00000257215.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.358

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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.409+54C>T		intron_variant		ENST00000257215.10	NP_006124.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAGLA	ENST00000257215.10 linkuse as main transcript	c.409+54C>T		intron_variant		1	NM_006133.3	ENSP00000257215	P1
DAGLA	ENST00000540717.1 linkuse as main transcript	c.386+54C>T		intron_variant, NMD_transcript_variant		5		ENSP00000440264

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35792

AN:

152066

Hom.:

5456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0596

Gnomad AMI

AF:

0.352

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.0322

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.263

GnomAD4 exome

AF:

0.304

AC:

373292

AN:

1226466

Hom.:

61833

AF XY:

0.303

AC XY:

188263

AN XY:

622010

show subpopulations

Gnomad4 AFR exome

AF:

0.0536

Gnomad4 AMR exome

AF:

0.197

Gnomad4 ASJ exome

AF:

0.479

Gnomad4 EAS exome

AF:

0.0301

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.305

Gnomad4 NFE exome

AF:

0.336

Gnomad4 OTH exome

AF:

0.295

GnomAD4 genome

AF:

0.235

AC:

35783

AN:

152182

Hom.:

5456

Cov.:

AF XY:

0.233

AC XY:

17329

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0595

Gnomad4 AMR

AF:

0.230

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.0322

Gnomad4 SAS

AF:

0.178

Gnomad4 FIN

AF:

0.296

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.260

Alfa

AF:

0.328

Hom.:

5026

Bravo

AF:

0.226

Asia WGS

AF:

0.106

AC:

370

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.017

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over