Variant rs2570407 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000465654.5(MGAM):c.-3+9095C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,310 control chromosomes in the GnomAD database, including 42,752 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 0.75 ( 42752 hom., cov: 27)

Consequence

MGAM
ENST00000465654.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.885

Variant links:

Genes affected

MGAM (HGNC:7043): (maltase-glucoamylase) This gene encodes maltase-glucoamylase, which is a brush border membrane enzyme that plays a role in the final steps of digestion of starch. The protein has two catalytic sites identical to those of sucrase-isomaltase, but the proteins are only 59% homologous. Both are members of glycosyl hydrolase family 31, which has a variety of substrate specificities. [provided by RefSeq, Jul 2008]

MGAM links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.141955092C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000465654.5 linkuse as main transcript	c.-3+9095C>A		intron_variant		3		ENSP00000419372.1		E7EW87

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113294

AN:

151194

Hom.:

42703

Cov.:

show subpopulations

Gnomad AFR

AF:

0.820

Gnomad AMI

AF:

0.842

Gnomad AMR

AF:

0.715

Gnomad ASJ

AF:

0.733

Gnomad EAS

AF:

0.710

Gnomad SAS

AF:

0.763

Gnomad FIN

AF:

0.736

Gnomad MID

AF:

0.740

Gnomad NFE

AF:

0.718

Gnomad OTH

AF:

0.745

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

GnomAD4 genome

AF:

0.749

AC:

113399

AN:

151310

Hom.:

42752

Cov.:

AF XY:

0.749

AC XY:

55354

AN XY:

73904

show subpopulations

Gnomad4 AFR

AF:

0.820

Gnomad4 AMR

AF:

0.716

Gnomad4 ASJ

AF:

0.733

Gnomad4 EAS

AF:

0.711

Gnomad4 SAS

AF:

0.762

Gnomad4 FIN

AF:

0.736

Gnomad4 NFE

AF:

0.718

Gnomad4 OTH

AF:

0.741

Alfa

AF:

0.721

Hom.:

42509

Bravo

AF:

0.750

Asia WGS

AF:

0.712

AC:

2475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.37

DANN

Benign

0.18

Splicing

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