6-37670786-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153487.4(MDGA1):​c.68-6680G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,034 control chromosomes in the GnomAD database, including 3,131 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 0.18 ( 3131 hom., cov: 32)

Consequence

MDGA1
NM_153487.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0330
Variant links:
Genes affected
MDGA1 (HGNC:19267): (MAM domain containing glycosylphosphatidylinositol anchor 1) This gene encodes a glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein that is expressed predominantly in the developing nervous system. In addition to possessing several cell adhesion molecule-like domains, the mature protein has six Ig-like domains, a single fibronectin type III domain, a MAM domain and a C-terminal GPI-anchoring site. Studies in other mammals suggest this protein plays a role in cell adhesion, migration, and axon guidance and, in the developing brain, neuronal migration. In humans, this gene is associated with bipolar disorder and schizophrenia. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MDGA1NM_153487.4 linkuse as main transcriptc.68-6680G>A intron_variant ENST00000434837.8 NP_705691.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MDGA1ENST00000434837.8 linkuse as main transcriptc.68-6680G>A intron_variant 1 NM_153487.4 ENSP00000402584 P1Q8NFP4-1

Frequencies

GnomAD3 genomes
AF:
0.177
AC:
26866
AN:
151914
Hom.:
3121
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.298
Gnomad AMI
AF:
0.0603
Gnomad AMR
AF:
0.169
Gnomad ASJ
AF:
0.143
Gnomad EAS
AF:
0.355
Gnomad SAS
AF:
0.255
Gnomad FIN
AF:
0.199
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.0856
Gnomad OTH
AF:
0.187
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.177
AC:
26908
AN:
152034
Hom.:
3131
Cov.:
32
AF XY:
0.184
AC XY:
13663
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.298
Gnomad4 AMR
AF:
0.169
Gnomad4 ASJ
AF:
0.143
Gnomad4 EAS
AF:
0.355
Gnomad4 SAS
AF:
0.256
Gnomad4 FIN
AF:
0.199
Gnomad4 NFE
AF:
0.0856
Gnomad4 OTH
AF:
0.187
Alfa
AF:
0.103
Hom.:
1364
Bravo
AF:
0.182
Asia WGS
AF:
0.294
AC:
1021
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.2
DANN
Benign
0.65

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.

Other links and lift over

dbSNP: rs7769372; hg19: chr6-37638562; API