14-46920083-T-A

Variant names:

• chr14-46920083-T-A
• rs778588739
• NM_001113498.3:c.2167A>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001113498.3(MDGA2):​c.2167A>T​(p.Ser723Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MDGA2 NM_001113498.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.88
• Publications: 0 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: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2921588).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MDGA2	NM_001113498.3	c.2167A>T	p.Ser723Cys	missense_variant	Exon 10 of 17	ENST00000399232.8	NP_001106970.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MDGA2	ENST00000399232.8	c.2167A>T	p.Ser723Cys	missense_variant	Exon 10 of 17	1	NM_001113498.3	ENSP00000382178.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 23, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1960A>T (p.T654S) alteration is located in exon 9 (coding exon 9) of the MDGA2 gene. This alteration results from a A to T substitution at nucleotide position 1960, causing the threonine (T) at amino acid position 654 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.069	T
BayesDel_noAF	Benign	-0.34
CADD	Pathogenic	30
DANN	Uncertain	0.98
DEOGEN2	Benign	0.049	.;.;T
Eigen	Uncertain	0.19
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.88	D;T;D
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.29	T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	0.69	.;.;N
PhyloP100		3.9
PrimateAI	Uncertain	0.60	T
PROVEAN	Benign	-0.30	N;N;.
REVEL	Benign	0.20
Sift	Benign	0.060	T;T;.
Sift4G	Uncertain	0.037	.;D;.
Polyphen		0.90	.;.;P
Vest4		0.55
MutPred		0.51		.;.;Gain of catalytic residue at L655 (P = 0);
MVP		0.31
MPC		0.34
ClinPred		0.78	D
GERP RS		4.2
Varity_R		0.079
gMVP		0.57
Mutation Taster		=93/7	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs778588739; hg19: chr14-47389286;