rs12703441

chr7-142192907-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAM2	NM_001293626.2	c.4347-3247A>G		intron_variant		ENST00000477922.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAM2	ENST00000477922.4	c.4347-3247A>G		intron_variant		5	NM_001293626.2	P1
MGAM2	ENST00000496337.1	n.1267-3247A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.377

Alfa AF: 0.404 Hom.: 3354

Bravo AF: 0.392

Asia WGS AF: 0.460 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.2
Dann	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs12703441; hg19: chr7-141892707;