11-61723014-C-T

Variant names:

• chr11-61723014-C-T
• rs198426
• NM_006133.3:c.409+54C>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.409+54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 1,378,648 control chromosomes in the GnomAD database, including 67,289 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 0.24 (5456 hom., cov: 33)
  • Exomes 𝑓: 0.30 (61833 hom.)
• Consequence: DAGLA NM_006133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 28 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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.409+54C>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.409+54C>T		intron	N/A	ENSP00000257215.5	Q9Y4D2
	DAGLA	ENST00000875660.1		c.409+54C>T		intron	N/A	ENSP00000545719.1
	DAGLA	ENST00000939714.1		c.409+54C>T		intron	N/A	ENSP00000609773.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35792 AN: 152066 Hom.: 5456 Cov.: 33

Gnomad AFR AF: 0.0596

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.0322

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.263

GnomAD4 exome AF: 0.304 AC: 373292 AN: 1226466 Hom.: 61833 AF XY: 0.303 AC XY: 188263 AN XY: 622010

African (AFR) AF: 0.0536 AC: 1547 AN: 28838

American (AMR) AF: 0.197 AC: 8720 AN: 44238

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 11747 AN: 24502

East Asian (EAS) AF: 0.0301 AC: 1162 AN: 38636

South Asian (SAS) AF: 0.185 AC: 15044 AN: 81464

European-Finnish (FIN) AF: 0.305 AC: 16032 AN: 52642

Middle Eastern (MID) AF: 0.392 AC: 2087 AN: 5326

European-Non Finnish (NFE) AF: 0.336 AC: 301393 AN: 898050

Other (OTH) AF: 0.295 AC: 15560 AN: 52770

GnomAD4 genome AF: 0.235 AC: 35783 AN: 152182 Hom.: 5456 Cov.: 33 AF XY: 0.233 AC XY: 17329 AN XY: 74402

African (AFR) AF: 0.0595 AC: 2471 AN: 41536

American (AMR) AF: 0.230 AC: 3522 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3468

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5180

South Asian (SAS) AF: 0.178 AC: 856 AN: 4820

European-Finnish (FIN) AF: 0.296 AC: 3134 AN: 10582

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22996 AN: 67986

Other (OTH) AF: 0.260 AC: 548 AN: 2108

Alfa AF: 0.302 Hom.: 18185

Bravo AF: 0.226

Asia WGS AF: 0.106 AC: 370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.017
DANN	Benign	0.44
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs198426; hg19: chr11-61490486;