rs836518

Positions:

• chr7-6423015-G-A
• chr7-6423015-G-T

Variant summary

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

The NM_139179.4(DAGLB):​c.1141-1211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,136 control chromosomes in the GnomAD database, including 14,686 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 0.38 (14686 hom., cov: 33)
• Consequence: DAGLB NM_139179.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAGLB	NM_139179.4	c.1141-1211C>T		intron_variant		ENST00000297056.11	NP_631918.3
DAGLB	NM_001142936.2	c.754-1211C>T		intron_variant			NP_001136408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAGLB	ENST00000297056.11	c.1141-1211C>T		intron_variant		1	NM_139179.4	ENSP00000297056.6
DAGLB	ENST00000436575.5	c.1018-1211C>T		intron_variant		2		ENSP00000404785.1
DAGLB	ENST00000425398.6	c.754-1211C>T		intron_variant		2		ENSP00000391171.2
DAGLB	ENST00000454738.5	n.*63-1211C>T		intron_variant		2		ENSP00000411746.1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58378 AN: 152018 Hom.: 14643 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.358

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.384 AC: 58488 AN: 152136 Hom.: 14686 Cov.: 33 AF XY: 0.390 AC XY: 29029 AN XY: 74364

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.363

Alfa AF: 0.240 Hom.: 8097

Bravo AF: 0.410

Asia WGS AF: 0.542 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.52

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: rs836518; hg19: chr7-6462646;