rs12870
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030765.4(B3GNT4):c.*885T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000222 in 1,352,408 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 8.3e-7 ( 0 hom. )
Consequence
B3GNT4
NM_030765.4 3_prime_UTR
NM_030765.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.220
Genes affected
DIABLO (HGNC:21528): (diablo IAP-binding mitochondrial protein) This gene encodes an inhibitor of apoptosis protein (IAP)-binding protein. The encoded mitochondrial protein enters the cytosol when cells undergo apoptosis, and allows activation of caspases by binding to inhibitor of apoptosis proteins. Overexpression of the encoded protein sensitizes tumor cells to apoptosis. A mutation in this gene is associated with young-adult onset of nonsyndromic deafness-64. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]
B3GNT4 (HGNC:15683): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase protein family. The encoded enzyme is involved in the biosynthesis of poly-N-acetyllactosamine chains and prefers lacto-N-neotetraose as a substrate. It is a type II transmembrane protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIABLO | NM_001371333.1 | c.*108A>T | 3_prime_UTR_variant | 6/6 | ENST00000464942.7 | ||
B3GNT4 | NM_030765.4 | c.*885T>A | 3_prime_UTR_variant | 3/3 | ENST00000324189.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GNT4 | ENST00000324189.5 | c.*885T>A | 3_prime_UTR_variant | 3/3 | 1 | NM_030765.4 | A2 | ||
DIABLO | ENST00000464942.7 | c.*108A>T | 3_prime_UTR_variant | 6/6 | 1 | NM_001371333.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151958Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000482 AC: 1AN: 207302Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 113462
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GnomAD4 exome AF: 8.33e-7 AC: 1AN: 1200450Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0AN XY: 606962
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151958Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74210
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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