Genetic Variant MDGA2:p.Ile369Ile (chr14-47096942-G-A) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2

The NM_001113498.3(MDGA2):c.1107C>T(p.Ile369Ile) variant causes a synonymous change. The variant allele was found at a frequency of 0.00331 in 1,613,310 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 21 hom. )

Consequence

MDGA2
NM_001113498.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.23

Variant links:

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]

MDGA2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.186).

BP6

Variant 14-47096942-G-A is Benign according to our data. Variant chr14-47096942-G-A is described in ClinVar as [Benign]. Clinvar id is 774712.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 21 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MDGA2	NM_001113498.3 link	c.1107C>T	p.Ile369Ile	synonymous_variant	Exon 6 of 17	ENST00000399232.8	NP_001106970.4	Q7Z553-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MDGA2	ENST00000399232.8 link	c.1107C>T	p.Ile369Ile	synonymous_variant	Exon 6 of 17	1	NM_001113498.3	ENSP00000382178.4		Q7Z553-3

Frequencies

GnomAD3 genomes

AF:

0.00266

AC:

404

AN:

151986

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000435

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00230

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.00706

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00381

Gnomad OTH

AF:

0.00144

GnomAD2 exomes

AF:

0.00277

AC:

690

AN:

249030

AF XY:

0.00297

show subpopulations

Gnomad AFR exome

AF:

0.000775

Gnomad AMR exome

AF:

0.00180

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00589

Gnomad NFE exome

AF:

0.00365

Gnomad OTH exome

AF:

0.00231

GnomAD4 exome

AF:

0.00338

AC:

4932

AN:

1461206

Hom.:

Cov.:

AF XY:

0.00331

AC XY:

2407

AN XY:

726926

show subpopulations

Gnomad4 AFR exome

AF:

0.000598

AC:

AN:

33450

Gnomad4 AMR exome

AF:

0.00181

AC:

AN:

44668

Gnomad4 ASJ exome

AF:

0.000383

AC:

AN:

26094

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

39692

Gnomad4 SAS exome

AF:

0.00206

AC:

178

AN:

86246

Gnomad4 FIN exome

AF:

0.00556

AC:

297

AN:

53416

Gnomad4 NFE exome

AF:

0.00374

AC:

4153

AN:

1111510

Gnomad4 Remaining exome

AF:

0.00292

AC:

176

AN:

60364

Heterozygous variant carriers

270

540

809

1079

1349

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

146

292

438

584

730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00266

AC:

405

AN:

152104

Hom.:

Cov.:

AF XY:

0.00295

AC XY:

219

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.000433

AC:

0.000433338

AN:

0.000433338

Gnomad4 AMR

AF:

0.00230

AC:

0.00229538

AN:

0.00229538

Gnomad4 ASJ

AF:

0.000577

AC:

0.000577367

AN:

0.000577367

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00270

AC:

0.0026971

AN:

0.0026971

Gnomad4 FIN

AF:

0.00706

AC:

0.00706348

AN:

0.00706348

Gnomad4 NFE

AF:

0.00381

AC:

0.00381219

AN:

0.00381219

Gnomad4 OTH

AF:

0.00142

AC:

0.00142315

AN:

0.00142315

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00317

Hom.:

Bravo

AF:

0.00244

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Aug 04, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.78

Mutation Taster

=98/2

polymorphism

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over