rs8132770
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001356336.2(B3GALT5):c.-160-5796A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,108 control chromosomes in the GnomAD database, including 19,651 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 0.51 ( 19651 hom., cov: 33)
Consequence
B3GALT5
NM_001356336.2 intron
NM_001356336.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.98
Genes affected
B3GALT5 (HGNC:920): (beta-1,3-galactosyltransferase 5) This gene encodes a member of a family of membrane-bound glycoproteins. The encoded protein may synthesize type 1 Lewis antigens, which are elevated in gastrointestinal and pancreatic cancers. Alternatively spliced transcript variants using multiple alternate promoters have been observed for this gene. [provided by RefSeq, Sep 2017]
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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=-1.0).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B3GALT5 | NM_001356336.2 | c.-160-5796A>T | intron_variant | ENST00000684187.2 | |||
B3GALT5 | NM_001278650.2 | c.-160-5796A>T | intron_variant | ||||
B3GALT5 | NM_001356338.2 | c.-160-5796A>T | intron_variant | ||||
B3GALT5 | NM_001356339.2 | c.-160-5796A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GALT5 | ENST00000684187.2 | c.-160-5796A>T | intron_variant | NM_001356336.2 | P1 | ||||
ENST00000416555.1 | n.220+23467A>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.506 AC: 76916AN: 151990Hom.: 19633 Cov.: 33
GnomAD3 genomes
?
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151990
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.506 AC: 76975AN: 152108Hom.: 19651 Cov.: 33 AF XY: 0.509 AC XY: 37846AN XY: 74354
GnomAD4 genome
?
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AC:
76975
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152108
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33
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37846
AN XY:
74354
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Asia WGS
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1886
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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