rs1298582

Variant names:

• chr7-142007730-A-T
• rs1298582
• NM_001365693.1:c.128-776A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365693.1(MGAM):​c.128-776A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,966 control chromosomes in the GnomAD database, including 26,295 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 0.58 (26295 hom., cov: 32)
• Consequence: MGAM NM_001365693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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 = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365693.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAM	NM_001365693.1	MANE Select	c.128-776A>T		intron	N/A	NP_001352622.1
	MGAM	NM_004668.3		c.128-776A>T		intron	N/A	NP_004659.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAM	ENST00000475668.6	TSL:5 MANE Select	c.128-776A>T		intron	N/A	ENSP00000417515.2
	MGAM	ENST00000549489.6	TSL:1	c.128-776A>T		intron	N/A	ENSP00000447378.2
	MGAM	ENST00000620571.1	TSL:5	c.128-776A>T		intron	N/A	ENSP00000482292.1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87810 AN: 151846 Hom.: 26263 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.578 AC: 87893 AN: 151966 Hom.: 26295 Cov.: 32 AF XY: 0.581 AC XY: 43191 AN XY: 74286

African (AFR) AF: 0.712 AC: 29532 AN: 41466

American (AMR) AF: 0.509 AC: 7757 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1786 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4018 AN: 5170

South Asian (SAS) AF: 0.464 AC: 2236 AN: 4820

European-Finnish (FIN) AF: 0.626 AC: 6608 AN: 10550

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.502 AC: 34142 AN: 67948

Other (OTH) AF: 0.540 AC: 1140 AN: 2110

Alfa AF: 0.559 Hom.: 3078

Bravo AF: 0.577

Asia WGS AF: 0.645 AC: 2237 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.73
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1298582; hg19: chr7-141707530;