3-127775021-C-T

Position:

• chr3-127775021-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007283.7(MGLL):​c.262+6768G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,108 control chromosomes in the GnomAD database, including 56,737 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 0.86 (56737 hom., cov: 31)
• Consequence: MGLL NM_007283.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

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]

MGLL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGLL	NM_007283.7	c.262+6768G>A		intron_variant		ENST00000265052.10	NP_009214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGLL	ENST00000265052.10	c.262+6768G>A		intron_variant		1	NM_007283.7	ENSP00000265052.5

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130834 AN: 151990 Hom.: 56688 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.861 AC: 130938 AN: 152108 Hom.: 56737 Cov.: 31 AF XY: 0.855 AC XY: 63575 AN XY: 74356

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.878

Alfa AF: 0.875 Hom.: 80508

Bravo AF: 0.859

Asia WGS AF: 0.723 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.28

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: rs567384; hg19: chr3-127493864;