ENST00000465654.5:c.-3+9095C>A

Variant names:

• chr7-141955092-C-A
• rs2570407
• ENST00000465654.5:c.-3+9095C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000465654.5(MGAM):​c.-3+9095C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,310 control chromosomes in the GnomAD database, including 42,752 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 0.75 (42752 hom., cov: 27)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 9 publications found

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]

MGAM Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000465654.5	c.-3+9095C>A		intron_variant	Intron 2 of 5	3		ENSP00000419372.1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113294 AN: 151194 Hom.: 42703 Cov.: 27

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.740

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.749 AC: 113399 AN: 151310 Hom.: 42752 Cov.: 27 AF XY: 0.749 AC XY: 55354 AN XY: 73904

African (AFR) AF: 0.820 AC: 33791 AN: 41206

American (AMR) AF: 0.716 AC: 10851 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2535 AN: 3460

East Asian (EAS) AF: 0.711 AC: 3641 AN: 5120

South Asian (SAS) AF: 0.762 AC: 3644 AN: 4780

European-Finnish (FIN) AF: 0.736 AC: 7701 AN: 10464

Middle Eastern (MID) AF: 0.759 AC: 220 AN: 290

European-Non Finnish (NFE) AF: 0.718 AC: 48710 AN: 67838

Other (OTH) AF: 0.741 AC: 1540 AN: 2078

Alfa AF: 0.724 Hom.: 56657

Bravo AF: 0.750

Asia WGS AF: 0.712 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.18
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs2570407; hg19: chr7-141654892;