rs504697
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007355.4(HSP90AB1):c.1731+72T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 1,407,296 control chromosomes in the GnomAD database, including 360,627 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 0.73 ( 40229 hom., cov: 32)
Exomes 𝑓: 0.71 ( 320398 hom. )
Consequence
HSP90AB1
NM_007355.4 intron
NM_007355.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.378
Genes affected
HSP90AB1 (HGNC:5258): (heat shock protein 90 alpha family class B member 1) This gene encodes a member of the heat shock protein 90 family; these proteins are involved in signal transduction, protein folding and degradation and morphological evolution. This gene encodes the constitutive form of the cytosolic 90 kDa heat-shock protein and is thought to play a role in gastric apoptosis and inflammation. Alternative splicing results in multiple transcript variants. Pseudogenes have been identified on multiple chromosomes. [provided by RefSeq, Dec 2012]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSP90AB1 | NM_007355.4 | c.1731+72T>C | intron_variant | ENST00000371646.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSP90AB1 | ENST00000371646.10 | c.1731+72T>C | intron_variant | 1 | NM_007355.4 | P1 | |||
HSP90AB1 | ENST00000353801.7 | c.1731+72T>C | intron_variant | 1 | P1 | ||||
HSP90AB1 | ENST00000371554.2 | c.1731+72T>C | intron_variant | 5 | P1 | ||||
HSP90AB1 | ENST00000620073.4 | c.1731+72T>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.726 AC: 110392AN: 151958Hom.: 40195 Cov.: 32
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GnomAD4 exome AF: 0.713 AC: 895295AN: 1255220Hom.: 320398 AF XY: 0.714 AC XY: 450068AN XY: 630328
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GnomAD4 genome ? AF: 0.726 AC: 110480AN: 152076Hom.: 40229 Cov.: 32 AF XY: 0.728 AC XY: 54124AN XY: 74334
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at