rs886038734
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152490.5(B3GALNT2):c.-20G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000189 in 1,484,854 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000060 ( 0 hom. )
Consequence
B3GALNT2
NM_152490.5 5_prime_UTR
NM_152490.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.14
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 1-235504272-C-G is Benign according to our data. Variant chr1-235504272-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 262648.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B3GALNT2 | NM_152490.5 | c.-20G>C | 5_prime_UTR_variant | 1/12 | ENST00000366600.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GALNT2 | ENST00000366600.8 | c.-20G>C | 5_prime_UTR_variant | 1/12 | 1 | NM_152490.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152134Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000231 AC: 2AN: 86702Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 49228
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GnomAD4 exome AF: 0.00000600 AC: 8AN: 1332612Hom.: 0 Cov.: 33 AF XY: 0.00000456 AC XY: 3AN XY: 657416
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GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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