7-142011099-T-C

Variant names:

• chr7-142011099-T-C
• rs1527307
• NM_001365693.1:c.327+2394T>C

Variant summary

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

The NM_001365693.1(MGAM):​c.327+2394T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,132 control chromosomes in the GnomAD database, including 37,181 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 0.69 (37181 hom., cov: 33)
• Consequence: MGAM NM_001365693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAM	NM_001365693.1	MANE Select	c.327+2394T>C		intron	N/A	NP_001352622.1	O43451-2
	MGAM	NM_004668.3		c.327+2394T>C		intron	N/A	NP_004659.2	O43451-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAM	ENST00000475668.6	TSL:5 MANE Select	c.327+2394T>C		intron	N/A	ENSP00000417515.2	O43451-2
	MGAM	ENST00000549489.6	TSL:1	c.327+2394T>C		intron	N/A	ENSP00000447378.2	O43451-1
	MGAM	ENST00000620571.1	TSL:5	c.327+2394T>C		intron	N/A	ENSP00000482292.1	O43451-1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105249 AN: 152012 Hom.: 37131 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.692 AC: 105349 AN: 152132 Hom.: 37181 Cov.: 33 AF XY: 0.693 AC XY: 51529 AN XY: 74364

African (AFR) AF: 0.784 AC: 32539 AN: 41522

American (AMR) AF: 0.623 AC: 9512 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2261 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5127 AN: 5176

South Asian (SAS) AF: 0.621 AC: 2990 AN: 4814

European-Finnish (FIN) AF: 0.709 AC: 7503 AN: 10588

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43171 AN: 67968

Other (OTH) AF: 0.670 AC: 1414 AN: 2112

Alfa AF: 0.646 Hom.: 45674

Bravo AF: 0.693

Asia WGS AF: 0.814 AC: 2827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.24
PhyloP100		-1.4
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: rs1527307; hg19: chr7-141710899;