rs2236647
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006819.3(STIP1):c.673-138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 1,097,512 control chromosomes in the GnomAD database, including 120,404 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 0.52 ( 22188 hom., cov: 31)
Exomes 𝑓: 0.45 ( 98216 hom. )
Consequence
STIP1
NM_006819.3 intron
NM_006819.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.33
Genes affected
STIP1 (HGNC:11387): (stress induced phosphoprotein 1) STIP1 is an adaptor protein that coordinates the functions of HSP70 (see HSPA1A; MIM 140550) and HSP90 (see HSP90AA1; MIM 140571) in protein folding. It is thought to assist in the transfer of proteins from HSP70 to HSP90 by binding both HSP90 and substrate-bound HSP70. STIP1 also stimulates the ATPase activity of HSP70 and inhibits the ATPase activity of HSP90, suggesting that it regulates both the conformations and ATPase cycles of these chaperones (Song and Masison, 2005 [PubMed 16100115]).[supplied by OMIM, Jul 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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STIP1 | NM_006819.3 | c.673-138C>T | intron_variant | ENST00000305218.9 | |||
STIP1 | NM_001282652.2 | c.814-138C>T | intron_variant | ||||
STIP1 | NM_001282653.2 | c.601-138C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STIP1 | ENST00000305218.9 | c.673-138C>T | intron_variant | 1 | NM_006819.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.523 AC: 79318AN: 151780Hom.: 22149 Cov.: 31
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GnomAD4 exome AF: 0.451 AC: 426347AN: 945614Hom.: 98216 Cov.: 12 AF XY: 0.452 AC XY: 215146AN XY: 475752
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GnomAD4 genome ? AF: 0.523 AC: 79407AN: 151898Hom.: 22188 Cov.: 31 AF XY: 0.520 AC XY: 38606AN XY: 74252
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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