rs2011138

Variant names:

• chr3-127825086-C-A
• rs2011138
• ENST00000648300.1:n.-21+580G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-127825086-C-A
• chr3-127825086-C-T

Variant summary

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

The ENST00000648300.1(MGLL):​n.-21+580G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 141,348 control chromosomes in the GnomAD database, including 9,749 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 0.38 (9749 hom., cov: 22)
• Consequence: MGLL ENST00000648300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714
• Publications: 2 publications found

Genes affected

MGLL (HGNC:17038): (monoglyceride lipase) This gene encodes a serine hydrolase of the AB hydrolase superfamily that catalyzes the conversion of monoacylglycerides to free fatty acids and glycerol. The encoded protein plays a critical role in several physiological processes including pain and nociperception through hydrolysis of the endocannabinoid 2-arachidonoylglycerol. Expression of this gene may play a role in cancer tumorigenesis and metastasis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

ENSG00000287143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGLL	ENST00000648300.1	n.-21+580G>T		intron_variant	Intron 5 of 12			ENSP00000497905.1
ENSG00000287143	ENST00000785485.1	n.144+3331C>A		intron_variant	Intron 1 of 3
ENSG00000302312	ENST00000785719.1	n.167+2249C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 53175 AN: 141276 Hom.: 9750 Cov.: 22

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.376 AC: 53182 AN: 141348 Hom.: 9749 Cov.: 22 AF XY: 0.383 AC XY: 25938 AN XY: 67772

African (AFR) AF: 0.337 AC: 12798 AN: 37936

American (AMR) AF: 0.365 AC: 4757 AN: 13040

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1635 AN: 3410

East Asian (EAS) AF: 0.404 AC: 1932 AN: 4780

South Asian (SAS) AF: 0.538 AC: 2358 AN: 4386

European-Finnish (FIN) AF: 0.417 AC: 3555 AN: 8518

Middle Eastern (MID) AF: 0.500 AC: 120 AN: 240

European-Non Finnish (NFE) AF: 0.376 AC: 24881 AN: 66212

Other (OTH) AF: 0.389 AC: 752 AN: 1932

Alfa AF: 0.197 Hom.: 382

Bravo AF: 0.355

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.76
PhyloP100		0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2011138; hg19: chr3-127543929; COSMIC: COSV54023682;