chr19-55274407-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_012267.5(HSPBP1):c.631G>T(p.Ala211Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000346 in 1,155,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000035 ( 0 hom. )
Consequence
HSPBP1
NM_012267.5 missense
NM_012267.5 missense
Scores
10
6
1
Clinical Significance
Conservation
PhyloP100: 6.51
Genes affected
HSPBP1 (HGNC:24989): (HSPA (Hsp70) binding protein 1) Enables ubiquitin protein ligase binding activity. Involved in positive regulation of proteasomal ubiquitin-dependent protein catabolic process and positive regulation of protein ubiquitination. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.786
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPBP1 | NM_012267.5 | c.631G>T | p.Ala211Ser | missense_variant | 4/8 | ENST00000433386.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPBP1 | ENST00000433386.7 | c.631G>T | p.Ala211Ser | missense_variant | 4/8 | 1 | NM_012267.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
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30
GnomAD3 exomes AF: 0.00000567 AC: 1AN: 176518Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 97286
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GnomAD4 exome AF: 0.00000346 AC: 4AN: 1155974Hom.: 0 Cov.: 36 AF XY: 0.00000527 AC XY: 3AN XY: 569058
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GnomAD4 genome Cov.: 30
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30
ExAC
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2022 | The c.631G>T (p.A211S) alteration is located in exon 4 (coding exon 3) of the HSPBP1 gene. This alteration results from a G to T substitution at nucleotide position 631, causing the alanine (A) at amino acid position 211 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
T;T;T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;.;.;.
REVEL
Uncertain
Sift
Pathogenic
D;D;.;.;.
Sift4G
Pathogenic
D;D;D;.;D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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