dbSNP rs702485: 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139179.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAGLB	NM_139179.4	MANE Select	c.*196T>C		3_prime_UTR	Exon 15 of 15	NP_631918.3	Q8NCG7-1
	DAGLB	NM_001142936.2		c.*196T>C		3_prime_UTR	Exon 13 of 13	NP_001136408.1	Q8NCG7-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DAGLB	ENST00000297056.11	TSL:1 MANE Select	c.*196T>C	3_prime_UTR	Exon 15 of 15	ENSP00000297056.6	Q8NCG7-1
DAGLB	ENST00000878465.1		c.*196T>C	3_prime_UTR	Exon 16 of 16	ENSP00000548524.1
DAGLB	ENST00000878464.1		c.*196T>C	3_prime_UTR	Exon 15 of 15	ENSP00000548523.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over