Variant 7-6409132-G-C 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.*705C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 153,048 control chromosomes in the GnomAD database, including 28,855 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 0.59 ( 28742 hom., cov: 32)

Exomes 𝑓: 0.44 ( 113 hom. )

Consequence

DAGLB
NM_139179.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.67

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAGLB	NM_139179.4 link	c.*705C>G		3_prime_UTR_variant	15/15	ENST00000297056.11	NP_631918.3	Q8NCG7-1
DAGLB	NM_001142936.2 link	c.*705C>G		3_prime_UTR_variant	13/13		NP_001136408.1	Q8NCG7-4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DAGLB	ENST00000297056 link	c.*705C>G	3_prime_UTR_variant	15/15	1	NM_139179.4	ENSP00000297056.6	Q8NCG7-1
DAGLB	ENST00000462934.5 link	n.2583C>G	non_coding_transcript_exon_variant	7/7	2
DAGLB	ENST00000482149.5 link	n.2376C>G	splice_region_variant, non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes

AF:

0.590

AC:

89704

AN:

151934

Hom.:

28676

Cov.:

show subpopulations

Gnomad AFR

AF:

0.813

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.627

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.910

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.551

GnomAD4 exome

AF:

0.445

AC:

443

AN:

996

Hom.:

113

Cov.:

AF XY:

0.433

AC XY:

231

AN XY:

534

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

0.571

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.614

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.414

Gnomad4 OTH exome

AF:

0.289

GnomAD4 genome

AF:

0.591

AC:

89835

AN:

152052

Hom.:

28742

Cov.:

AF XY:

0.595

AC XY:

44233

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.814

Gnomad4 AMR

AF:

0.628

Gnomad4 ASJ

AF:

0.344

Gnomad4 EAS

AF:

0.910

Gnomad4 SAS

AF:

0.640

Gnomad4 FIN

AF:

0.470

Gnomad4 NFE

AF:

0.453

Gnomad4 OTH

AF:

0.557

Alfa

AF:

0.360

Hom.:

906

Bravo

AF:

0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.071

DANN

Benign

0.45

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