2-134410029-G-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002410.5(MGAT5):​c.1531-2840G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,160 control chromosomes in the GnomAD database, including 5,674 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 0.25 ( 5674 hom., cov: 33)

Consequence

MGAT5
NM_002410.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.123

Publications

7 publications found
Variant links:
Genes affected
MGAT5 (HGNC:7049): (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase) The protein encoded by this gene belongs to the glycosyltransferase family. It catalyzes the addition of beta-1,6-N-acetylglucosamine to the alpha-linked mannose of biantennary N-linked oligosaccharides present on the newly synthesized glycoproteins. It is one of the most important enzymes involved in the regulation of the biosynthesis of glycoprotein oligosaccharides. Alterations of the oligosaccharides on cell surface glycoproteins cause significant changes in the adhesive or migratory behavior of a cell. Increase in the activity of this enzyme has been correlated with the progression of invasive malignancies. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MGAT5NM_002410.5 linkc.1531-2840G>A intron_variant Intron 11 of 15 ENST00000281923.4 NP_002401.1 Q09328

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MGAT5ENST00000281923.4 linkc.1531-2840G>A intron_variant Intron 11 of 15 1 NM_002410.5 ENSP00000281923.2 Q09328
MGAT5ENST00000409645.5 linkc.1531-2840G>A intron_variant Intron 12 of 16 5 ENSP00000386377.1 Q09328

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
38610
AN:
152040
Hom.:
5662
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.259
Gnomad AMR
AF:
0.335
Gnomad ASJ
AF:
0.368
Gnomad EAS
AF:
0.388
Gnomad SAS
AF:
0.465
Gnomad FIN
AF:
0.283
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.287
Gnomad OTH
AF:
0.267
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.254
AC:
38639
AN:
152160
Hom.:
5674
Cov.:
33
AF XY:
0.260
AC XY:
19372
AN XY:
74380
show subpopulations
African (AFR)
AF:
0.109
AC:
4546
AN:
41528
American (AMR)
AF:
0.336
AC:
5132
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.368
AC:
1277
AN:
3470
East Asian (EAS)
AF:
0.388
AC:
2005
AN:
5168
South Asian (SAS)
AF:
0.467
AC:
2248
AN:
4814
European-Finnish (FIN)
AF:
0.283
AC:
2998
AN:
10586
Middle Eastern (MID)
AF:
0.293
AC:
86
AN:
294
European-Non Finnish (NFE)
AF:
0.287
AC:
19542
AN:
67988
Other (OTH)
AF:
0.269
AC:
569
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1475
2950
4424
5899
7374
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
398
796
1194
1592
1990
<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:
0.282
Hom.:
11472
Bravo
AF:
0.248
Asia WGS
AF:
0.397
AC:
1383
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.9
DANN
Benign
0.21
PhyloP100
-0.12
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

Publications

Other links and lift over

dbSNP: rs2118844; hg19: chr2-135167600; API