Variant rs702485 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_139179.4(DAGLB):c.*196T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 684,868 control chromosomes in the GnomAD database, including 99,108 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 0.58 ( 27565 hom., cov: 31)

Exomes 𝑓: 0.50 ( 71543 hom. )

Consequence

DAGLB
NM_139179.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.02

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:

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 (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAGLB	NM_139179.4 linkuse as main transcript	c.*196T>C		3_prime_UTR_variant	15/15	ENST00000297056.11	NP_631918.3
DAGLB	NM_001142936.2 linkuse as main transcript	c.*196T>C		3_prime_UTR_variant	13/13		NP_001136408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAGLB	ENST00000297056.11 linkuse as main transcript	c.*196T>C		3_prime_UTR_variant	15/15	1	NM_139179.4	ENSP00000297056	P1	Q8NCG7-1

Frequencies

GnomAD3 genomes

AF:

0.579

AC:

87953

AN:

151934

Hom.:

27503

Cov.:

show subpopulations

Gnomad AFR

AF:

0.789

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.893

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.464

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.449

Gnomad OTH

AF:

0.543

GnomAD4 exome

AF:

0.501

AC:

266685

AN:

532816

Hom.:

71543

Cov.:

AF XY:

0.502

AC XY:

138142

AN XY:

275454

show subpopulations

Gnomad4 AFR exome

AF:

0.788

Gnomad4 AMR exome

AF:

0.657

Gnomad4 ASJ exome

AF:

0.346

Gnomad4 EAS exome

AF:

0.900

Gnomad4 SAS exome

AF:

0.578

Gnomad4 FIN exome

AF:

0.464

Gnomad4 NFE exome

AF:

0.443

Gnomad4 OTH exome

AF:

0.518

GnomAD4 genome

AF:

0.579

AC:

88080

AN:

152052

Hom.:

27565

Cov.:

AF XY:

0.584

AC XY:

43382

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.789

Gnomad4 AMR

AF:

0.621

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.893

Gnomad4 SAS

AF:

0.609

Gnomad4 FIN

AF:

0.464

Gnomad4 NFE

AF:

0.449

Gnomad4 OTH

AF:

0.549

Alfa

AF:

0.481

Hom.:

18435

Bravo

AF:

0.601

Asia WGS

AF:

0.797

AC:

2766

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.26

DANN

Benign

0.20

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over