NM_001365693.1:c.6810+810T>G

Variant names:

• chr7-142087527-T-G
• rs10464448
• NM_001365693.1:c.6810+810T>G

Variant summary

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

The NM_001365693.1(MGAM):​c.6810+810T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 144,796 control chromosomes in the GnomAD database, including 23,558 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 0.51 (23558 hom., cov: 28)
• Consequence: MGAM NM_001365693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAM	NM_001365693.1	c.6810+810T>G		intron_variant	Intron 57 of 70	ENST00000475668.6	NP_001352622.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAM	ENST00000475668.6	c.6810+810T>G		intron_variant	Intron 57 of 70	5	NM_001365693.1	ENSP00000417515.2
MGAM	ENST00000549489.6	c.4619-7093T>G		intron_variant	Intron 38 of 47	1		ENSP00000447378.2
MGAM	ENST00000620571.1	c.4771-8038T>G		intron_variant	Intron 40 of 47	5		ENSP00000482292.1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 73273 AN: 144678 Hom.: 23530 Cov.: 28

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.507 AC: 73341 AN: 144796 Hom.: 23558 Cov.: 28 AF XY: 0.500 AC XY: 35223 AN XY: 70416

African (AFR) AF: 0.674 AC: 27599 AN: 40940

American (AMR) AF: 0.357 AC: 5135 AN: 14394

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1584 AN: 3306

East Asian (EAS) AF: 0.428 AC: 2087 AN: 4880

South Asian (SAS) AF: 0.518 AC: 2354 AN: 4546

European-Finnish (FIN) AF: 0.431 AC: 4191 AN: 9728

Middle Eastern (MID) AF: 0.647 AC: 180 AN: 278

European-Non Finnish (NFE) AF: 0.452 AC: 28849 AN: 63878

Other (OTH) AF: 0.522 AC: 1046 AN: 2002

Alfa AF: 0.434 Hom.: 8305

Asia WGS AF: 0.531 AC: 1824 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.47
PhyloP100		-1.9
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: rs10464448; hg19: chr7-141787327;