chr11-61714574-C-T

Variant names:

• chr11-61714574-C-T
• rs198436
• NM_006133.3:c.-44-5538C>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.-44-5538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,196 control chromosomes in the GnomAD database, including 30,917 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 0.63 (30917 hom., cov: 33)
• Consequence: DAGLA NM_006133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66
• Publications: 4 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=-1.02).
• 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: NM_006133.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAGLA	NM_006133.3	MANE Select	c.-44-5538C>T		intron	N/A	NP_006124.1	Q9Y4D2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAGLA	ENST00000257215.10	TSL:1 MANE Select	c.-44-5538C>T		intron	N/A	ENSP00000257215.5	Q9Y4D2
	DAGLA	ENST00000875660.1		c.-44-5538C>T		intron	N/A	ENSP00000545719.1
	DAGLA	ENST00000971001.1		c.-44-5538C>T		intron	N/A	ENSP00000641060.1

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96144 AN: 152078 Hom.: 30882 Cov.: 33

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.632 AC: 96236 AN: 152196 Hom.: 30917 Cov.: 33 AF XY: 0.638 AC XY: 47448 AN XY: 74408

African (AFR) AF: 0.554 AC: 22988 AN: 41522

American (AMR) AF: 0.704 AC: 10775 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4901 AN: 5190

South Asian (SAS) AF: 0.749 AC: 3611 AN: 4822

European-Finnish (FIN) AF: 0.663 AC: 7028 AN: 10598

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.635 AC: 43181 AN: 67972

Other (OTH) AF: 0.627 AC: 1324 AN: 2112

Alfa AF: 0.635 Hom.: 39893

Bravo AF: 0.630

Asia WGS AF: 0.814 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.027
DANN	Benign	0.52
PhyloP100		-3.7
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: rs198436; hg19: chr11-61482046;