NM_001113498.3:c.281-104611G>T

Variant names:

• chr14-47406161-C-A
• rs2416065
• NM_001113498.3:c.281-104611G>T

Variant summary

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

The NM_001113498.3(MDGA2):​c.281-104611G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 151,944 control chromosomes in the GnomAD database, including 39,546 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 0.72 (39546 hom., cov: 32)
• Consequence: MDGA2 NM_001113498.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 1 publications found

Genes affected

MDGA2 (HGNC:19835): (MAM domain containing glycosylphosphatidylinositol anchor 2) Predicted to be involved in regulation of presynapse assembly; regulation of synaptic membrane adhesion; and spinal cord motor neuron differentiation. Predicted to act upstream of or within neuron migration and pattern specification process. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in GABA-ergic synapse and glutamatergic synapse. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001113498.3. 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
	MDGA2	NM_001113498.3	MANE Select	c.281-104611G>T		intron	N/A	NP_001106970.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MDGA2	ENST00000399232.8	TSL:1 MANE Select	c.281-104611G>T		intron	N/A	ENSP00000382178.4
	MDGA2	ENST00000557238.5	TSL:5	n.-614-104611G>T		intron	N/A	ENSP00000452593.1

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108752 AN: 151826 Hom.: 39520 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.716 AC: 108831 AN: 151944 Hom.: 39546 Cov.: 32 AF XY: 0.723 AC XY: 53715 AN XY: 74272

African (AFR) AF: 0.624 AC: 25859 AN: 41432

American (AMR) AF: 0.767 AC: 11709 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2312 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5163 AN: 5170

South Asian (SAS) AF: 0.843 AC: 4066 AN: 4824

European-Finnish (FIN) AF: 0.776 AC: 8197 AN: 10566

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.725 AC: 49249 AN: 67916

Other (OTH) AF: 0.696 AC: 1464 AN: 2104

Alfa AF: 0.646 Hom.: 2095

Bravo AF: 0.713

Asia WGS AF: 0.903 AC: 3107 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.23
PhyloP100		-0.44
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: rs2416065; hg19: chr14-47875364;