rs547647945

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_021996.6(GBGT1):​c.466G>C​(p.Gly156Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,444,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

GBGT1
NM_021996.6 missense

Scores

17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.631
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06845778).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GBGT1NM_021996.6 linkc.466G>C p.Gly156Arg 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.466G>C p.Gly156Arg missense_variant Exon 7 of 7 1 NM_021996.6 ENSP00000361110.3 Q8N5D6-1
ENSG00000285245ENST00000647146.1 linkc.396+1023G>C intron_variant Intron 6 of 22 ENSP00000493691.1 A0A2R8Y471

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.92e-7
AC:
1
AN:
1444428
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
714848
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:
9.10e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.064
BayesDel_addAF
Benign
-0.39
T
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.052
DANN
Benign
0.40
DEOGEN2
Benign
0.010
T;.
Eigen
Benign
-1.9
Eigen_PC
Benign
-1.8
FATHMM_MKL
Benign
0.040
N
LIST_S2
Benign
0.36
T;T
M_CAP
Benign
0.0062
T
MetaRNN
Benign
0.068
T;T
MetaSVM
Benign
-0.91
T
PROVEAN
Benign
1.5
N;N
REVEL
Benign
0.0030
Sift
Benign
1.0
T;T
Sift4G
Benign
0.67
T;T
Polyphen
0.0
B;.
Vest4
0.039
MutPred
0.32
Loss of catalytic residue at V157 (P = 0.0154);.;
MVP
0.21
MPC
0.10
ClinPred
0.026
T
GERP RS
-1.9
Varity_R
0.026
gMVP
0.38

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-136029542; API