rs11767947

Variant names:

• chr7-141912821-G-A
• rs11767947
• ENST00000465654.5:c.-180+4953G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-141912821-G-A
• chr7-141912821-G-T

Variant summary

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

The ENST00000465654.5(MGAM):​c.-180+4953G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,010 control chromosomes in the GnomAD database, including 4,903 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 0.23 (4903 hom., cov: 32)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465654.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAM	ENST00000465654.5	TSL:3	c.-180+4953G>A		intron	N/A	ENSP00000419372.1
	MGAM	ENST00000497554.1	TSL:3	n.36+4953G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35095 AN: 151892 Hom.: 4905 Cov.: 32

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.231 AC: 35093 AN: 152010 Hom.: 4903 Cov.: 32 AF XY: 0.233 AC XY: 17340 AN XY: 74290

African (AFR) AF: 0.0750 AC: 3110 AN: 41478

American (AMR) AF: 0.317 AC: 4838 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2280 AN: 5160

South Asian (SAS) AF: 0.237 AC: 1142 AN: 4818

European-Finnish (FIN) AF: 0.275 AC: 2887 AN: 10516

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19187 AN: 67970

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.263 Hom.: 14387

Bravo AF: 0.230

Asia WGS AF: 0.337 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11767947; hg19: chr7-141612621;