rs11762634

chr7-141956687-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAM	ENST00000465654.5	c.-3+10690G>A		intron_variant		3

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

Gnomad4 AFR AF: 0.0692

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.241

Alfa AF: 0.279 Hom.: 4192

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11762634; hg19: chr7-141656487;