17-49163131-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001159387.2(B4GALNT2):c.767-957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,904 control chromosomes in the GnomAD database, including 3,179 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 0.19 ( 3179 hom., cov: 30)
Consequence
B4GALNT2
NM_001159387.2 intron
NM_001159387.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.392
Genes affected
B4GALNT2 (HGNC:24136): (beta-1,4-N-acetyl-galactosaminyltransferase 2 (SID blood group)) B4GALNT2 catalyzes the last step in the biosynthesis of the human Sd(a) antigen through the addition of an N-acetylgalactosamine residue via a beta-1,4 linkage to a subterminal galactose residue substituted with an alpha-2,3-linked sialic acid. B4GALNT2 also catalyzes the last step in the biosynthesis of the Cad antigen (Montiel et al., 2003 [PubMed 12678917]).[supplied by OMIM, Mar 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=-0.93).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B4GALNT2 | NM_001159387.2 | c.767-957G>A | intron_variant | ENST00000393354.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B4GALNT2 | ENST00000393354.7 | c.767-957G>A | intron_variant | 1 | NM_001159387.2 | P1 | |||
B4GALNT2 | ENST00000300404.2 | c.947-957G>A | intron_variant | 1 | |||||
B4GALNT2 | ENST00000504681.5 | c.689-957G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.190 AC: 28872AN: 151786Hom.: 3169 Cov.: 30
GnomAD3 genomes
?
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28872
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151786
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.190 AC: 28897AN: 151904Hom.: 3179 Cov.: 30 AF XY: 0.192 AC XY: 14245AN XY: 74242
GnomAD4 genome
?
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AC:
28897
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151904
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30
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14245
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74242
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1103
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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