rs702485

chr7-6409641-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02

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]

ACMG classification

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	UniProt
DAGLB	NM_139179.4	c.*196T>C		3_prime_UTR_variant	15/15	ENST00000297056.11
DAGLB	NM_001142936.2	c.*196T>C		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAGLB	ENST00000297056.11	c.*196T>C		3_prime_UTR_variant	15/15	1	NM_139179.4	P1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87953 AN: 151934 Hom.: 27503 Cov.: 31

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.: 6 AF XY: 0.502 AC XY: 138142 AN XY: 275454

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.: 31 AF XY: 0.584 AC XY: 43382 AN XY: 74328

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

Other links and lift over

dbSNP: rs702485; hg19: chr7-6449272; COSMIC: COSV51702377; COSMIC: COSV51702377;