rs17162635

Variant names:

• chr7-141978163-T-A
• rs17162635
• ENST00000465654.5:c.-2-27366T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-141978163-T-A
• chr7-141978163-T-G

Variant summary

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

The ENST00000465654.5(MGAM):​c.-2-27366T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,086 control chromosomes in the GnomAD database, including 1,031 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 (1031 hom., cov: 32)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 5 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 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.-2-27366T>A		intron_variant	Intron 2 of 5	3		ENSP00000419372.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15708 AN: 151968 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.103 AC: 15713 AN: 152086 Hom.: 1031 Cov.: 32 AF XY: 0.108 AC XY: 8004 AN XY: 74334

African (AFR) AF: 0.0371 AC: 1540 AN: 41500

American (AMR) AF: 0.0951 AC: 1452 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0879 AC: 305 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1350 AN: 5160

South Asian (SAS) AF: 0.152 AC: 732 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1927 AN: 10568

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8121 AN: 67982

Other (OTH) AF: 0.104 AC: 219 AN: 2110

Alfa AF: 0.111 Hom.: 143

Bravo AF: 0.0949

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.4
DANN	Benign	0.73
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs17162635; hg19: chr7-141677963;