rs7144383

Variant names:

• chr14-47571172-G-A
• rs7144383
• NM_001113498.3:c.280+103345C>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.280+103345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,284 control chromosomes in the GnomAD database, including 65,166 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 0.92 (65166 hom., cov: 33)
• Consequence: MDGA2 NM_001113498.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 13 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=-0.96).
• 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.280+103345C>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.280+103345C>T		intron	N/A	ENSP00000382178.4
	MDGA2	ENST00000557238.5	TSL:5	n.-615+55167C>T		intron	N/A	ENSP00000452593.1

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140616 AN: 152166 Hom.: 65115 Cov.: 33

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.924 AC: 140726 AN: 152284 Hom.: 65166 Cov.: 33 AF XY: 0.928 AC XY: 69104 AN XY: 74454

African (AFR) AF: 0.979 AC: 40691 AN: 41578

American (AMR) AF: 0.932 AC: 14257 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3088 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5173 AN: 5178

South Asian (SAS) AF: 0.952 AC: 4599 AN: 4832

European-Finnish (FIN) AF: 0.929 AC: 9862 AN: 10614

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60065 AN: 67996

Other (OTH) AF: 0.911 AC: 1926 AN: 2114

Alfa AF: 0.907 Hom.: 7756

Bravo AF: 0.926

Asia WGS AF: 0.982 AC: 3412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.61
PhyloP100		-0.84
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: rs7144383; hg19: chr14-48040375;