NM_001293626.2:c.4347-3247A>G

Variant names:

• chr7-142192907-A-G
• rs12703441
• NM_001293626.2:c.4347-3247A>G

Variant summary

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

The NM_001293626.2(MGAM2):​c.4347-3247A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,130 control chromosomes in the GnomAD database, including 11,944 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 0.39 (11944 hom., cov: 32)
• Consequence: MGAM2 NM_001293626.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704
• Publications: 4 publications found

Genes affected

MGAM2 (HGNC:28101): (maltase-glucoamylase 2 (putative)) Predicted to enable alpha-1,4-glucosidase activity. Predicted to be involved in carbohydrate metabolic process. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001293626.2. 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
	MGAM2	NM_001293626.2	MANE Select	c.4347-3247A>G		intron	N/A	NP_001280555.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAM2	ENST00000477922.4	TSL:5 MANE Select	c.4347-3247A>G		intron	N/A	ENSP00000420449.3
	MGAM2	ENST00000496337.1	TSL:5	n.1267-3247A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59272 AN: 152012 Hom.: 11941 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.390 AC: 59302 AN: 152130 Hom.: 11944 Cov.: 32 AF XY: 0.393 AC XY: 29244 AN XY: 74342

African (AFR) AF: 0.300 AC: 12445 AN: 41500

American (AMR) AF: 0.481 AC: 7350 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2533 AN: 5170

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4388 AN: 10566

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27739 AN: 68006

Other (OTH) AF: 0.377 AC: 797 AN: 2112

Alfa AF: 0.406 Hom.: 7236

Bravo AF: 0.392

Asia WGS AF: 0.460 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		0.70
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: rs12703441; hg19: chr7-141892707;