rs11762634

Variant names:

• chr7-141956687-G-A
• rs11762634
• ENST00000465654.5:c.-3+10690G>A

Variant summary

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

The ENST00000465654.5(MGAM):​c.-3+10690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,988 control chromosomes in the GnomAD database, including 4,571 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 0.22 (4571 hom., cov: 32)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000465654.5	c.-3+10690G>A		intron_variant	Intron 2 of 5	3		ENSP00000419372.1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33942 AN: 151870 Hom.: 4568 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.223 AC: 33943 AN: 151988 Hom.: 4571 Cov.: 32 AF XY: 0.225 AC XY: 16731 AN XY: 74280

African (AFR) AF: 0.0692 AC: 2870 AN: 41482

American (AMR) AF: 0.298 AC: 4545 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1647 AN: 5166

South Asian (SAS) AF: 0.240 AC: 1157 AN: 4824

European-Finnish (FIN) AF: 0.274 AC: 2880 AN: 10528

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19178 AN: 67948

Other (OTH) AF: 0.241 AC: 508 AN: 2108

Alfa AF: 0.275 Hom.: 5305

Bravo AF: 0.219

Asia WGS AF: 0.285 AC: 989 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.67
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11762634; hg19: chr7-141656487;