rs4963243

Positions:

• chr11-61726855-G-A

Variant summary

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

The NM_006133.3(DAGLA):​c.636+773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,292 control chromosomes in the GnomAD database, including 1,306 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 0.11 (1306 hom., cov: 33)
• Consequence: DAGLA NM_006133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

DAGLA (HGNC:1165): (diacylglycerol lipase alpha) This gene encodes a diacylglycerol lipase. The encoded enzyme is involved in the biosynthesis of the endocannabinoid 2-arachidonoyl-glycerol.[provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAGLA	NM_006133.3	c.636+773G>A		intron_variant		ENST00000257215.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAGLA	ENST00000257215.10	c.636+773G>A		intron_variant		1	NM_006133.3	P1
DAGLA	ENST00000540717.1	c.*109+773G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17206 AN: 152174 Hom.: 1308 Cov.: 33

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.113 AC: 17209 AN: 152292 Hom.: 1306 Cov.: 33 AF XY: 0.115 AC XY: 8564 AN XY: 74464

Gnomad4 AFR AF: 0.0343

Gnomad4 AMR AF: 0.0820

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.118

Alfa AF: 0.139 Hom.: 3106

Bravo AF: 0.105

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs4963243; hg19: chr11-61494327;