11-61714574-C-T

Position:

• chr11-61714574-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAGLA	NM_006133.3	c.-44-5538C>T		intron_variant		ENST00000257215.10	NP_006124.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAGLA	ENST00000257215.10	c.-44-5538C>T		intron_variant		1	NM_006133.3	ENSP00000257215.5
DAGLA	ENST00000540717.1	n.-44-5538C>T		intron_variant		5		ENSP00000440264.1

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

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.627

Alfa AF: 0.580 Hom.: 2823

Bravo AF: 0.630

Asia WGS AF: 0.814 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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