Genetic Variant DAGLB:c.*705C>G (chr7-6409132-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

14 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DAGLB	NM_139179.4 link	c.*705C>G		3_prime_UTR_variant	Exon 15 of 15	ENST00000297056.11	NP_631918.3
DAGLB	NM_001142936.2 link	c.*705C>G		3_prime_UTR_variant	Exon 13 of 13		NP_001136408.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
DAGLB	ENST00000297056.11 link	c.*705C>G	3_prime_UTR_variant	Exon 15 of 15	1	NM_139179.4	ENSP00000297056.6
DAGLB	ENST00000462934.5 link	n.2583C>G	non_coding_transcript_exon_variant	Exon 7 of 7	2
DAGLB	ENST00000482149.5 link	n.2376C>G	splice_region_variant, non_coding_transcript_exon_variant	Exon 6 of 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

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.571

AC:

AN:

156

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.614

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.414

AC:

308

AN:

744

Other (OTH)

AF:

0.289

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.591

AC:

89835

AN:

152052

Hom.:

28742

Cov.:

AF XY:

0.595

AC XY:

44233

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.814

AC:

33777

AN:

41512

American (AMR)

AF:

0.628

AC:

9589

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

1196

AN:

3472

East Asian (EAS)

AF:

0.910

AC:

4685

AN:

5146

South Asian (SAS)

AF:

0.640

AC:

3081

AN:

4814

European-Finnish (FIN)

AF:

0.470

AC:

4966

AN:

10558

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.453

AC:

30777

AN:

67954

Other (OTH)

AF:

0.557

AC:

1175

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1654

3308

4961

6615

8269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

734

1468

2202

2936

3670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.45

PhyloP100

-4.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over