9-113360674-A-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_017688.3(BSPRY):āc.468A>Gā(p.Lys156=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 1,606,006 control chromosomes in the GnomAD database, including 52,617 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: š 0.31 ( 8344 hom., cov: 32)
Exomes š: 0.24 ( 44273 hom. )
Consequence
BSPRY
NM_017688.3 synonymous
NM_017688.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.08
Genes affected
BSPRY (HGNC:18232): (B-box and SPRY domain containing) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein ubiquitination. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in cell leading edge; membrane; and perinuclear region of cytoplasm. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
Synonymous conserved (PhyloP=1.08 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BSPRY | NM_017688.3 | c.468A>G | p.Lys156= | synonymous_variant | 3/6 | ENST00000374183.5 | |
BSPRY | NM_001317943.2 | c.468A>G | p.Lys156= | synonymous_variant | 3/6 | ||
BSPRY | NM_001317944.2 | c.468A>G | p.Lys156= | synonymous_variant | 3/5 | ||
BSPRY | XM_006717149.4 | c.468A>G | p.Lys156= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BSPRY | ENST00000374183.5 | c.468A>G | p.Lys156= | synonymous_variant | 3/6 | 1 | NM_017688.3 | P1 | |
BSPRY | ENST00000462085.1 | n.506A>G | non_coding_transcript_exon_variant | 3/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.305 AC: 46354AN: 151932Hom.: 8300 Cov.: 32
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GnomAD3 exomes AF: 0.263 AC: 62259AN: 237162Hom.: 9302 AF XY: 0.256 AC XY: 32895AN XY: 128736
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GnomAD4 exome AF: 0.236 AC: 343715AN: 1453956Hom.: 44273 Cov.: 35 AF XY: 0.237 AC XY: 171085AN XY: 722652
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GnomAD4 genome AF: 0.306 AC: 46456AN: 152050Hom.: 8344 Cov.: 32 AF XY: 0.304 AC XY: 22570AN XY: 74338
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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