9-133155205-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021996.6(GBGT1):āc.332T>Cā(p.Ile111Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000497 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00021 ( 0 hom., cov: 32)
Exomes š: 0.00053 ( 0 hom. )
Consequence
GBGT1
NM_021996.6 missense
NM_021996.6 missense
Scores
1
4
13
Clinical Significance
Conservation
PhyloP100: 5.42
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=0.20744157).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GBGT1 | NM_021996.6 | c.332T>C | p.Ile111Thr | missense_variant | 6/7 | ENST00000372040.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GBGT1 | ENST00000372040.9 | c.332T>C | p.Ile111Thr | missense_variant | 6/7 | 1 | NM_021996.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000211 AC: 32AN: 151884Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000239 AC: 60AN: 250968Hom.: 1 AF XY: 0.000184 AC XY: 25AN XY: 135808
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GnomAD4 exome AF: 0.000527 AC: 770AN: 1461746Hom.: 0 Cov.: 32 AF XY: 0.000499 AC XY: 363AN XY: 727188
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GnomAD4 genome AF: 0.000211 AC: 32AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74306
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 06, 2021 | The c.332T>C (p.I111T) alteration is located in exon 6 (coding exon 5) of the GBGT1 gene. This alteration results from a T to C substitution at nucleotide position 332, causing the isoleucine (I) at amino acid position 111 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
M;M;.;.
MutationTaster
Benign
D;D;D;D;D
PROVEAN
Uncertain
D;D;.;D
REVEL
Benign
Sift
Uncertain
D;D;.;D
Sift4G
Uncertain
D;D;.;D
Polyphen
P;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at