dbSNP rs782444: MGLL:c.*1100A>G (chr3-127691098-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007283.7(MGLL):c.*1100A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,570 control chromosomes in the GnomAD database, including 21,092 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 0.52 ( 21036 hom., cov: 34)

Exomes 𝑓: 0.46 ( 56 hom. )

Consequence

MGLL
NM_007283.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.810

Publications

15 publications found

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:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007283.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MGLL	NM_007283.7	MANE Select	c.*1100A>G	3_prime_UTR	Exon 8 of 8	NP_009214.1	A0A0C4DFN3
MGLL	NM_001388312.1		c.*1100A>G	3_prime_UTR	Exon 9 of 9	NP_001375241.1
MGLL	NM_001388313.1		c.*1100A>G	3_prime_UTR	Exon 9 of 9	NP_001375242.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MGLL	ENST00000265052.10	TSL:1 MANE Select	c.*1100A>G	3_prime_UTR	Exon 8 of 8	ENSP00000265052.5	A0A0C4DFN3
MGLL	ENST00000864851.1		c.*1100A>G	3_prime_UTR	Exon 9 of 9	ENSP00000534910.1
MGLL	ENST00000398104.6	TSL:5	c.*1100A>G	3_prime_UTR	Exon 8 of 8	ENSP00000381176.1	Q99685-1

Frequencies

GnomAD3 genomes

AF:

0.522

AC:

79257

AN:

151928

Hom.:

21031

Cov.:

show subpopulations

Gnomad AFR

AF:

0.469

Gnomad AMI

AF:

0.476

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.422

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.555

GnomAD4 exome

AF:

0.462

AC:

242

AN:

524

Hom.:

Cov.:

AF XY:

0.500

AC XY:

163

AN XY:

326

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.435

AC:

187

AN:

430

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.608

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.521

AC:

79291

AN:

152046

Hom.:

21036

Cov.:

AF XY:

0.516

AC XY:

38314

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.468

AC:

19434

AN:

41484

American (AMR)

AF:

0.558

AC:

8528

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

1851

AN:

3472

East Asian (EAS)

AF:

0.673

AC:

3453

AN:

5134

South Asian (SAS)

AF:

0.491

AC:

2367

AN:

4824

European-Finnish (FIN)

AF:

0.422

AC:

4479

AN:

10604

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.551

AC:

37415

AN:

67918

Other (OTH)

AF:

0.550

AC:

1163

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1999

3997

5996

7994

9993

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

706

1412

2118

2824

3530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.542

Hom.:

27277

Bravo

AF:

0.531

Asia WGS

AF:

0.576

AC:

2005

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.68

(source)

DANN

Benign

0.72

PhyloP100

-0.81

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over