NM_006133.3:c.-45+15793C>T

Variant names:

• chr11-61696297-C-T
• rs60507107
• NM_006133.3:c.-45+15793C>T

Variant summary

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

The NM_006133.3(DAGLA):​c.-45+15793C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,144 control chromosomes in the GnomAD database, including 2,334 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 0.17 (2334 hom., cov: 32)
• Consequence: DAGLA NM_006133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 6 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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006133.3. 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+15793C>T		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+15793C>T		intron	N/A	ENSP00000257215.5
	DAGLA	ENST00000540717.1	TSL:5	n.-45+15793C>T		intron	N/A	ENSP00000440264.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25312 AN: 152024 Hom.: 2333 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.167 AC: 25344 AN: 152144 Hom.: 2334 Cov.: 32 AF XY: 0.167 AC XY: 12426 AN XY: 74374

African (AFR) AF: 0.212 AC: 8792 AN: 41518

American (AMR) AF: 0.104 AC: 1596 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1371 AN: 5146

South Asian (SAS) AF: 0.127 AC: 614 AN: 4820

European-Finnish (FIN) AF: 0.199 AC: 2111 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9970 AN: 67972

Other (OTH) AF: 0.166 AC: 351 AN: 2110

Alfa AF: 0.161 Hom.: 258

Bravo AF: 0.166

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.023
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: rs60507107; hg19: chr11-61463769;