rs17162635

Positions:

• chr7-141978163-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000465654.5(MGAM):​c.-2-27366T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,086 control chromosomes in the GnomAD database, including 1,031 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 0.10 (1031 hom., cov: 32)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.141978163T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000465654.5	c.-2-27366T>A		intron_variant		3		ENSP00000419372.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15708 AN: 151968 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.103 AC: 15713 AN: 152086 Hom.: 1031 Cov.: 32 AF XY: 0.108 AC XY: 8004 AN XY: 74334

Gnomad4 AFR AF: 0.0371

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.104

Alfa AF: 0.103 Hom.: 80

Bravo AF: 0.0949

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17162635; hg19: chr7-141677963;