rs11767119

chr7-141912316-G-Achr7-141912316-G-T

Variant summary

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

The ENST00000465654.5(MGAM):c.-180+4448G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,978 control chromosomes in the GnomAD database, including 4,957 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 0.24 (4957 hom., cov: 32)
• Consequence: MGAM ENST00000465654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAM	ENST00000465654.5	c.-180+4448G>A		intron_variant		3
MGAM	ENST00000497554.1	n.36+4448G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35802 AN: 151860 Hom.: 4958 Cov.: 32

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.236 AC: 35802 AN: 151978 Hom.: 4957 Cov.: 32 AF XY: 0.238 AC XY: 17669 AN XY: 74274

Gnomad4 AFR AF: 0.0916

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.250

Alfa AF: 0.275 Hom.: 1318

Bravo AF: 0.236

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.2
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11767119; hg19: chr7-141612116;