rs702485

Variant names:

• chr7-6409641-A-G
• rs702485
• NM_139179.4:c.*196T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 66 publications found

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

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	c.*196T>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000297056.11	NP_631918.3
DAGLB	NM_001142936.2	c.*196T>C		3_prime_UTR_variant	Exon 13 of 13		NP_001136408.1

Ensembl

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

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

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

GnomAD4 genome AF: 0.579 AC: 88080 AN: 152052 Hom.: 27565 Cov.: 31 AF XY: 0.584 AC XY: 43382 AN XY: 74328

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

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
DANN	Benign	0.20
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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