rs2204607

Positions:

• chr7-142009894-C-T

Variant summary

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

The NM_001365693.1(MGAM):​c.327+1189C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,108 control chromosomes in the GnomAD database, including 891 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 (891 hom., cov: 32)
• Consequence: MGAM NM_001365693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAM	NM_001365693.1	c.327+1189C>T		intron_variant		ENST00000475668.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAM	ENST00000475668.6	c.327+1189C>T		intron_variant		5	NM_001365693.1	P1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15365 AN: 151990 Hom.: 891 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0907

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.101 AC: 15368 AN: 152108 Hom.: 891 Cov.: 32 AF XY: 0.0981 AC XY: 7294 AN XY: 74348

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.0904

Gnomad4 FIN AF: 0.0811

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.106

Alfa AF: 0.105 Hom.: 142

Bravo AF: 0.103

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs2204607; hg19: chr7-141709694;