rs59405398
Your query was ambiguous. Multiple possible variants found:
- chr1-235448220-CAAAAAAAAAAAA-C
- chr1-235448220-CAAAAAAAAAAAA-CA
- chr1-235448220-CAAAAAAAAAAAA-CAA
- chr1-235448220-CAAAAAAAAAAAA-CAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAA
- chr1-235448220-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152490.5(B3GALNT2):c.*1974_*1985delTTTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
B3GALNT2
NM_152490.5 3_prime_UTR
NM_152490.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.65
Genes affected
B3GALNT2 (HGNC:28596): (beta-1,3-N-acetylgalactosaminyltransferase 2) This gene encodes a member of the glycosyltransferase 31 family. The encoded protein synthesizes GalNAc:beta-1,3GlcNAc, a novel carbohydrate structure, on N- and O-glycans. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Mar 2013]
TBCE (HGNC:11582): (tubulin folding cofactor E) Cofactor E is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
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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 |
---|---|---|---|---|---|---|---|---|
B3GALNT2 | NM_152490.5 | c.*1974_*1985delTTTTTTTTTTTT | 3_prime_UTR_variant | Exon 12 of 12 | ENST00000366600.8 | NP_689703.1 | ||
TBCE | NM_003193.5 | c.1400-120_1400-109delAAAAAAAAAAAA | intron_variant | Intron 15 of 16 | ENST00000642610.2 | NP_003184.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GALNT2 | ENST00000366600 | c.*1974_*1985delTTTTTTTTTTTT | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_152490.5 | ENSP00000355559.3 | |||
TBCE | ENST00000642610.2 | c.1400-120_1400-109delAAAAAAAAAAAA | intron_variant | Intron 15 of 16 | NM_003193.5 | ENSP00000494796.1 | ||||
ENSG00000285053 | ENST00000645655.1 | c.1400-120_1400-109delAAAAAAAAAAAA | intron_variant | Intron 18 of 19 | ENSP00000495202.1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 genomes
Cov.:
24
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 465430Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 252260
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
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465430
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0
AN XY:
252260
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GnomAD4 genome Cov.: 24
GnomAD4 genome
Cov.:
24
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at