rs1527304

Variant names:

• chr7-142009405-A-G
• rs1527304
• NM_001365693.1:c.327+700A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-142009405-A-G
• chr7-142009405-A-T

Variant summary

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

The NM_001365693.1(MGAM):​c.327+700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,982 control chromosomes in the GnomAD database, including 16,067 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 0.44 (16067 hom., cov: 32)
• Consequence: MGAM NM_001365693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAM	NM_001365693.1	c.327+700A>G		intron_variant	Intron 3 of 70	ENST00000475668.6	NP_001352622.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000475668.6	c.327+700A>G		intron_variant	Intron 3 of 70	5	NM_001365693.1	ENSP00000417515.2

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67227 AN: 151864 Hom.: 16063 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.443 AC: 67255 AN: 151982 Hom.: 16067 Cov.: 32 AF XY: 0.450 AC XY: 33382 AN XY: 74264

African (AFR) AF: 0.271 AC: 11245 AN: 41474

American (AMR) AF: 0.449 AC: 6841 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3476 AN: 5146

South Asian (SAS) AF: 0.448 AC: 2164 AN: 4826

European-Finnish (FIN) AF: 0.624 AC: 6583 AN: 10558

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33646 AN: 67954

Other (OTH) AF: 0.439 AC: 925 AN: 2108

Alfa AF: 0.471 Hom.: 3086

Bravo AF: 0.422

Asia WGS AF: 0.566 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.67
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1527304; hg19: chr7-141709205;