3-127744765-C-A

Variant names:

• chr3-127744765-C-A
• rs6787155
• NM_007283.7:c.263-22199G>T

Variant summary

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

The NM_007283.7(MGLL):​c.263-22199G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,106 control chromosomes in the GnomAD database, including 48,130 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 0.79 (48130 hom., cov: 32)
• Consequence: MGLL NM_007283.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• Publications: 4 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]

ENSG00000302344 (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 (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGLL	NM_007283.7	c.263-22199G>T		intron_variant	Intron 3 of 7	ENST00000265052.10	NP_009214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGLL	ENST00000265052.10	c.263-22199G>T		intron_variant	Intron 3 of 7	1	NM_007283.7	ENSP00000265052.5

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120786 AN: 151986 Hom.: 48078 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.795 AC: 120892 AN: 152106 Hom.: 48130 Cov.: 32 AF XY: 0.791 AC XY: 58808 AN XY: 74326

African (AFR) AF: 0.834 AC: 34592 AN: 41478

American (AMR) AF: 0.784 AC: 11990 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2640 AN: 3466

East Asian (EAS) AF: 0.809 AC: 4190 AN: 5180

South Asian (SAS) AF: 0.710 AC: 3415 AN: 4812

European-Finnish (FIN) AF: 0.760 AC: 8005 AN: 10536

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53507 AN: 68020

Other (OTH) AF: 0.800 AC: 1688 AN: 2110

Alfa AF: 0.789 Hom.: 118941

Bravo AF: 0.798

Asia WGS AF: 0.788 AC: 2744 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	3.7
DANN	Benign	0.48
PhyloP100		0.61
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: rs6787155; hg19: chr3-127463608;