11-61695916-A-G

Variant names:

• chr11-61695916-A-G
• rs198456
• NM_006133.3:c.-45+15412A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000257215.10(DAGLA):​c.-45+15412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,050 control chromosomes in the GnomAD database, including 33,381 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 0.66 (33381 hom., cov: 32)
• Consequence: DAGLA ENST00000257215.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000257215.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAGLA	NM_006133.3	MANE Select	c.-45+15412A>G		intron	N/A	NP_006124.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAGLA	ENST00000257215.10	TSL:1 MANE Select	c.-45+15412A>G		intron	N/A	ENSP00000257215.5
	DAGLA	ENST00000540717.1	TSL:5	n.-45+15412A>G		intron	N/A	ENSP00000440264.1

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100198 AN: 151932 Hom.: 33338 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.660 AC: 100301 AN: 152050 Hom.: 33381 Cov.: 32 AF XY: 0.664 AC XY: 49367 AN XY: 74326

African (AFR) AF: 0.647 AC: 26810 AN: 41468

American (AMR) AF: 0.716 AC: 10952 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3468

East Asian (EAS) AF: 0.944 AC: 4849 AN: 5138

South Asian (SAS) AF: 0.747 AC: 3602 AN: 4824

European-Finnish (FIN) AF: 0.664 AC: 7036 AN: 10598

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43239 AN: 67954

Other (OTH) AF: 0.655 AC: 1379 AN: 2106

Alfa AF: 0.643 Hom.: 121810

Bravo AF: 0.662

Asia WGS AF: 0.821 AC: 2856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.70
PhyloP100		0.039
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: rs198456; hg19: chr11-61463388;