Genetic Variant DAGLB:c.*196T>C (chr7-6409641-A-G) – 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.*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

Publications

66 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=-0.92).

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 rank	MANE	Protein	UniProt
DAGLB	NM_139179.4 link	c.*196T>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000297056.11	NP_631918.3	Q8NCG7-1
DAGLB	NM_001142936.2 link	c.*196T>C		3_prime_UTR_variant	Exon 13 of 13		NP_001136408.1	Q8NCG7-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAGLB	ENST00000297056.11 link	c.*196T>C		3_prime_UTR_variant	Exon 15 of 15	1	NM_139179.4	ENSP00000297056.6		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

African (AFR)

AF:

0.788

AC:

11052

AN:

14028

American (AMR)

AF:

0.657

AC:

11995

AN:

18244

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

4820

AN:

13948

East Asian (EAS)

AF:

0.900

AC:

27632

AN:

30712

South Asian (SAS)

AF:

0.578

AC:

27379

AN:

47350

European-Finnish (FIN)

AF:

0.464

AC:

13337

AN:

28764

Middle Eastern (MID)

AF:

0.433

AC:

1460

AN:

3368

European-Non Finnish (NFE)

AF:

0.443

AC:

154227

AN:

347870

Other (OTH)

AF:

0.518

AC:

14783

AN:

28532

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

6011

12021

18032

24042

30053

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2258

4516

6774

9032

11290

<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:

0.579

AC:

88080

AN:

152052

Hom.:

27565

Cov.:

AF XY:

0.584

AC XY:

43382

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.789

AC:

32747

AN:

41496

American (AMR)

AF:

0.621

AC:

9480

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.326

AC:

1129

AN:

3466

East Asian (EAS)

AF:

0.893

AC:

4619

AN:

5174

South Asian (SAS)

AF:

0.609

AC:

2937

AN:

4820

European-Finnish (FIN)

AF:

0.464

AC:

4906

AN:

10568

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.449

AC:

30520

AN:

67946

Other (OTH)

AF:

0.549

AC:

1160

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1745

3490

5235

6980

8725

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.506

Hom.:

58285

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

(source)

DANN

Benign

0.20

PhyloP100

-3.0

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