rs776225870

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_021996.6(GBGT1):ā€‹c.433T>Cā€‹(p.Tyr145His) variant causes a missense change. The variant allele was found at a frequency of 0.0000007 in 1,428,880 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 7.0e-7 ( 0 hom. )

Consequence

GBGT1
NM_021996.6 missense

Scores

1
7
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.94
Variant links:
Genes affected
GBGT1 (HGNC:20460): (globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group)) This gene encodes a glycosyltransferase that plays a role in the synthesis of Forssman glycolipid (FG), a member of the globoseries glycolipid family. Glycolipids such as FG form attachment sites for the binding of pathogens to cells; expression of this protein may determine host tropism to microorganisms. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GBGT1NM_021996.6 linkc.433T>C p.Tyr145His missense_variant Exon 7 of 7 ENST00000372040.9 NP_068836.2 Q8N5D6-1J7Q0Z1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GBGT1ENST00000372040.9 linkc.433T>C p.Tyr145His missense_variant Exon 7 of 7 1 NM_021996.6 ENSP00000361110.3 Q8N5D6-1
ENSG00000285245ENST00000647146.1 linkc.396+990T>C intron_variant Intron 6 of 22 ENSP00000493691.1 A0A2R8Y471

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000425
AC:
1
AN:
235048
Hom.:
0
AF XY:
0.00000787
AC XY:
1
AN XY:
127062
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000939
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
7.00e-7
AC:
1
AN:
1428880
Hom.:
0
Cov.:
31
AF XY:
0.00000142
AC XY:
1
AN XY:
705670
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.17e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
BayesDel_addAF
Benign
0.0041
T
BayesDel_noAF
Uncertain
0.060
CADD
Benign
22
DANN
Uncertain
1.0
Eigen
Uncertain
0.65
Eigen_PC
Uncertain
0.53
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.25
T;T
M_CAP
Uncertain
0.11
D
MetaRNN
Uncertain
0.45
T;T
MetaSVM
Benign
-1.1
T
PROVEAN
Benign
-1.2
.;N
REVEL
Benign
0.20
Sift
Pathogenic
0.0
.;D
Vest4
0.55
MutPred
0.35
Gain of loop (P = 0.0045);Gain of loop (P = 0.0045);
MVP
0.53
ClinPred
0.99
D
GERP RS
5.4

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: rs776225870; hg19: chr9-136029575; API