rs1045721
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_054025.3(B3GAT1):c.*1050C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 152,328 control chromosomes in the GnomAD database, including 914 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 0.091 ( 913 hom., cov: 33)
Exomes 𝑓: 0.14 ( 1 hom. )
Consequence
B3GAT1
NM_054025.3 3_prime_UTR
NM_054025.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.174
Genes affected
B3GAT1 (HGNC:921): (beta-1,3-glucuronyltransferase 1) The protein encoded by this gene is a member of the glucuronyltransferase gene family. These enzymes exhibit strict acceptor specificity, recognizing nonreducing terminal sugars and their anomeric linkages. This gene product functions as the key enzyme in a glucuronyl transfer reaction during the biosynthesis of the carbohydrate epitope HNK-1 (human natural killer-1, also known as CD57 and LEU7). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GAT1 | NM_054025.3 | c.*1050C>T | 3_prime_UTR_variant | 6/6 | ENST00000312527.9 | NP_473366.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GAT1 | ENST00000312527 | c.*1050C>T | 3_prime_UTR_variant | 6/6 | 1 | NM_054025.3 | ENSP00000307875.4 | |||
B3GAT1 | ENST00000392580 | c.*1050C>T | 3_prime_UTR_variant | 7/7 | 1 | ENSP00000376359.1 | ||||
B3GAT1 | ENST00000531778.1 | n.4952C>T | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0910 AC: 13839AN: 152002Hom.: 911 Cov.: 33
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GnomAD4 exome AF: 0.139 AC: 29AN: 208Hom.: 1 Cov.: 0 AF XY: 0.120 AC XY: 19AN XY: 158
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GnomAD4 genome AF: 0.0910 AC: 13850AN: 152120Hom.: 913 Cov.: 33 AF XY: 0.0919 AC XY: 6833AN XY: 74352
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at