chr7-142011099-T-C

Position:

• chr7-142011099-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAM	NM_001365693.1	c.327+2394T>C		intron_variant		ENST00000475668.6	NP_001352622.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000475668.6	c.327+2394T>C		intron_variant		5	NM_001365693.1	ENSP00000417515	P1

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

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.670

Alfa AF: 0.641 Hom.: 34089

Bravo AF: 0.693

Asia WGS AF: 0.814 AC: 2827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.24

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: rs1527307; hg19: chr7-141710899;