rs10516483
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017935.5(BANK1):c.903+104C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 1,310,130 control chromosomes in the GnomAD database, including 154,402 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 0.55 ( 24466 hom., cov: 31)
Exomes 𝑓: 0.47 ( 129936 hom. )
Consequence
BANK1
NM_017935.5 intron
NM_017935.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.228
Genes affected
BANK1 (HGNC:18233): (B cell scaffold protein with ankyrin repeats 1) The protein encoded by this gene is a B-cell-specific scaffold protein that functions in B-cell receptor-induced calcium mobilization from intracellular stores. This protein can also promote Lyn-mediated tyrosine phosphorylation of inositol 1,4,5-trisphosphate receptors. Polymorphisms in this gene are associated with susceptibility to systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BANK1 | NM_017935.5 | c.903+104C>G | intron_variant | ENST00000322953.9 | |||
BANK1 | NM_001083907.3 | c.813+104C>G | intron_variant | ||||
BANK1 | NM_001127507.3 | c.504+104C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BANK1 | ENST00000322953.9 | c.903+104C>G | intron_variant | 1 | NM_017935.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.552 AC: 83721AN: 151636Hom.: 24421 Cov.: 31
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GnomAD4 exome AF: 0.472 AC: 546313AN: 1158374Hom.: 129936 AF XY: 0.471 AC XY: 269638AN XY: 573056
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GnomAD4 genome ? AF: 0.552 AC: 83817AN: 151756Hom.: 24466 Cov.: 31 AF XY: 0.557 AC XY: 41276AN XY: 74152
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ClinVar
Not reported inComputational scores
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Name
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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