rs6104890
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080489.5(SDCBP2):c.732+612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,078 control chromosomes in the GnomAD database, including 42,378 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 0.74 ( 42378 hom., cov: 31)
Consequence
SDCBP2
NM_080489.5 intron
NM_080489.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0180
Genes affected
SDCBP2 (HGNC:15756): (syndecan binding protein 2) The protein encoded by this gene contains two class II PDZ domains. PDZ domains facilitate protein-protein interactions by binding to the cytoplasmic C-terminus of transmembrane proteins, and PDZ-containing proteins mediate cell signaling and the organization of protein complexes. The encoded protein binds to phosphatidylinositol 4, 5-bisphosphate (PIP2) and plays a role in nuclear PIP2 organization and cell division. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Read-through transcription also exists between this gene and the upstream FKBP1A (FK506 binding protein 1A, 12kDa) gene, as represented in GeneID:100528031. [provided by RefSeq, Sep 2011]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDCBP2 | NM_080489.5 | c.732+612G>A | intron_variant | ENST00000360779.4 | |||
FKBP1A-SDCBP2 | NR_037661.1 | n.1010+612G>A | intron_variant, non_coding_transcript_variant | ||||
SDCBP2 | NM_001199784.2 | c.732+612G>A | intron_variant | ||||
SDCBP2 | NM_015685.6 | c.477+612G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDCBP2 | ENST00000360779.4 | c.732+612G>A | intron_variant | 1 | NM_080489.5 | P1 | |||
SDCBP2 | ENST00000339987.7 | c.732+612G>A | intron_variant | 1 | P1 | ||||
SDCBP2 | ENST00000381808.7 | c.477+612G>A | intron_variant | 1 | |||||
SDCBP2 | ENST00000381812.5 | c.732+612G>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.740 AC: 112473AN: 151960Hom.: 42367 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.740 AC: 112518AN: 152078Hom.: 42378 Cov.: 31 AF XY: 0.747 AC XY: 55541AN XY: 74346
GnomAD4 genome
?
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55541
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74346
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2932
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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