chr7-141968603-G-T

Position:

• chr7-141968603-G-T

Variant summary

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

The ENST00000465654.5(MGAM):​c.-3+22606G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,460 control chromosomes in the GnomAD database, including 13,894 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 0.43 (13894 hom., cov: 32)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54

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=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000465654.5	c.-3+22606G>T		intron_variant		3		ENSP00000419372

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64513 AN: 151342 Hom.: 13871 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.426 AC: 64577 AN: 151460 Hom.: 13894 Cov.: 32 AF XY: 0.427 AC XY: 31583 AN XY: 73960

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.462

Alfa AF: 0.410 Hom.: 3316

Bravo AF: 0.443

Asia WGS AF: 0.417 AC: 1429 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4726481; hg19: chr7-141668403;