19-55274469-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_012267.5(HSPBP1):c.569G>A(p.Arg190His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000818 in 1,589,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R190S) has been classified as Uncertain significance.
Frequency
Consequence
NM_012267.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPBP1 | NM_012267.5 | c.569G>A | p.Arg190His | missense_variant | 4/8 | ENST00000433386.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPBP1 | ENST00000433386.7 | c.569G>A | p.Arg190His | missense_variant | 4/8 | 1 | NM_012267.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151712Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000495 AC: 1AN: 202206Hom.: 0 AF XY: 0.00000901 AC XY: 1AN XY: 110994
GnomAD4 exome AF: 0.00000557 AC: 8AN: 1437272Hom.: 0 Cov.: 36 AF XY: 0.00000280 AC XY: 2AN XY: 713702
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151828Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74200
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.569G>A (p.R190H) alteration is located in exon 4 (coding exon 3) of the HSPBP1 gene. This alteration results from a G to A substitution at nucleotide position 569, causing the arginine (R) at amino acid position 190 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at