Variant 7-142199898-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001293626.2(MGAM2):c.5067A>G(p.Gly1689Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 671,922 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 30)

Exomes 𝑓: 0.0015 ( 7 hom. )

Consequence

MGAM2
NM_001293626.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.255

Variant links:

Genes affected

MGAM2 (HGNC:28101): (maltase-glucoamylase 2 (putative)) Predicted to enable alpha-1,4-glucosidase activity. Predicted to be involved in carbohydrate metabolic process. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MGAM2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 7-142199898-A-G is Benign according to our data. Variant chr7-142199898-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2658105.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.255 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00152 (800/527790) while in subpopulation MID AF= 0.0289 (111/3840). AF 95% confidence interval is 0.0245. There are 7 homozygotes in gnomad4_exome. There are 476 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAM2	NM_001293626.2 link	c.5067A>G	p.Gly1689Gly	synonymous_variant	45/48	ENST00000477922.4	NP_001280555.1	Q2M2H8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAM2	ENST00000477922.4 link	c.5067A>G	p.Gly1689Gly	synonymous_variant	45/48	5	NM_001293626.2	ENSP00000420449.3		Q2M2H8-1
MGAM2	ENST00000496337.1 link	n.1987A>G		non_coding_transcript_exon_variant	18/22	5

Frequencies

GnomAD3 genomes

AF:

0.00103

AC:

149

AN:

144068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000286

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00257

Gnomad ASJ

AF:

0.00470

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00108

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0203

Gnomad NFE

AF:

0.000993

Gnomad OTH

AF:

0.00457

GnomAD3 exomes

AF:

0.00153

AC:

193

AN:

126094

Hom.:

AF XY:

0.00188

AC XY:

129

AN XY:

68584

show subpopulations

Gnomad AFR exome

AF:

0.000691

Gnomad AMR exome

AF:

0.00118

Gnomad ASJ exome

AF:

0.00473

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00297

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000957

Gnomad OTH exome

AF:

0.00497

GnomAD4 exome

AF:

0.00152

AC:

800

AN:

527790

Hom.:

Cov.:

AF XY:

0.00166

AC XY:

476

AN XY:

286494

show subpopulations

Gnomad4 AFR exome

AF:

0.000278

Gnomad4 AMR exome

AF:

0.00143

Gnomad4 ASJ exome

AF:

0.00483

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00266

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00105

Gnomad4 OTH exome

AF:

0.00238

GnomAD4 genome

AF:

0.00101

AC:

146

AN:

144132

Hom.:

Cov.:

AF XY:

0.000974

AC XY:

AN XY:

69794

show subpopulations

Gnomad4 AFR

AF:

0.000285

Gnomad4 AMR

AF:

0.00250

Gnomad4 ASJ

AF:

0.00470

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00109

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000993

Gnomad4 OTH

AF:

0.00455

Alfa

AF:

0.00128

Hom.:

Bravo

AF:

0.000948

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

MGAM2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

6.4

DANN

Benign

0.77

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over