7-141993008-T-G

Position:

• chr7-141993008-T-G

Variant summary

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

The ENST00000465654.5(MGAM):​c.-2-12521T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,144 control chromosomes in the GnomAD database, including 4,664 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 (4664 hom., cov: 32)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAM	XM_011516670.3	c.-3+4004T>G		intron_variant			XP_011514972.1
MGAM	XM_011516672.3	c.-3+3521T>G		intron_variant			XP_011514974.1
MGAM	XM_017012772.2	c.-3+4004T>G		intron_variant			XP_016868261.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000465654.5	c.-2-12521T>G		intron_variant		3		ENSP00000419372

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33142 AN: 152030 Hom.: 4643 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.218 AC: 33216 AN: 152144 Hom.: 4664 Cov.: 32 AF XY: 0.221 AC XY: 16403 AN XY: 74382

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.204

Alfa AF: 0.145 Hom.: 2463

Bravo AF: 0.230

Asia WGS AF: 0.293 AC: 1017 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6947481; hg19: chr7-141692808;