Variant 3-127821792-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2

The NM_007283.7(MGLL):c.57G>A(p.Arg19Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0354 in 1,613,988 control chromosomes in the GnomAD database, including 1,135 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 0.028 ( 90 hom., cov: 32)

Exomes 𝑓: 0.036 ( 1045 hom. )

Consequence

MGLL
NM_007283.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Variant links:

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 links:

MGLL (HGNC:):

MGLL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP7

Synonymous conserved (PhyloP=1.29 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0279 (4241/152212) while in subpopulation NFE AF= 0.0408 (2773/67992). AF 95% confidence interval is 0.0395. There are 90 homozygotes in gnomad4. There are 2062 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 90 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGLL	NM_007283.7 linkuse as main transcript	c.57G>A	p.Arg19Arg	synonymous_variant	2/8	ENST00000265052.10	NP_009214.1	Q99685A0A0C4DFN3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGLL	ENST00000265052.10 linkuse as main transcript	c.57G>A	p.Arg19Arg	synonymous_variant	2/8	1	NM_007283.7	ENSP00000265052.5		A0A0C4DFN3

Frequencies

GnomAD3 genomes

AF:

0.0279

AC:

4241

AN:

152096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00734

Gnomad AMI

AF:

0.0669

Gnomad AMR

AF:

0.0215

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0114

Gnomad FIN

AF:

0.0445

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0408

Gnomad OTH

AF:

0.0230

GnomAD3 exomes

AF:

0.0294

AC:

7332

AN:

249522

Hom.:

160

AF XY:

0.0298

AC XY:

4033

AN XY:

135370

show subpopulations

Gnomad AFR exome

AF:

0.00575

Gnomad AMR exome

AF:

0.0174

Gnomad ASJ exome

AF:

0.0487

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.0109

Gnomad FIN exome

AF:

0.0409

Gnomad NFE exome

AF:

0.0418

Gnomad OTH exome

AF:

0.0327

GnomAD4 exome

AF:

0.0362

AC:

52944

AN:

1461776

Hom.:

1045

Cov.:

AF XY:

0.0356

AC XY:

25899

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.00585

Gnomad4 AMR exome

AF:

0.0186

Gnomad4 ASJ exome

AF:

0.0512

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0117

Gnomad4 FIN exome

AF:

0.0414

Gnomad4 NFE exome

AF:

0.0407

Gnomad4 OTH exome

AF:

0.0329

GnomAD4 genome

AF:

0.0279

AC:

4241

AN:

152212

Hom.:

Cov.:

AF XY:

0.0277

AC XY:

2062

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.00732

Gnomad4 AMR

AF:

0.0214

Gnomad4 ASJ

AF:

0.0542

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0114

Gnomad4 FIN

AF:

0.0445

Gnomad4 NFE

AF:

0.0408

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.0374

Hom.:

Bravo

AF:

0.0255

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.0385

EpiControl

AF:

0.0420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

8.0

DANN

Benign

0.88

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over