19-55262626-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012267.5(HSPBP1):āc.1062C>Gā(p.Asp354Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_012267.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPBP1 | NM_012267.5 | c.1062C>G | p.Asp354Glu | missense_variant | 8/8 | ENST00000433386.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPBP1 | ENST00000433386.7 | c.1062C>G | p.Asp354Glu | missense_variant | 8/8 | 1 | NM_012267.5 | P1 | |
HSPBP1 | ENST00000255631.9 | c.1062C>G | p.Asp354Glu | missense_variant | 9/9 | 1 | P1 | ||
HSPBP1 | ENST00000587922.5 | c.1062C>G | p.Asp354Glu | missense_variant | 7/7 | 1 | P1 | ||
HSPBP1 | ENST00000585927.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250276Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135476
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461558Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727058
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.1062C>G (p.D354E) alteration is located in exon 8 (coding exon 7) of the HSPBP1 gene. This alteration results from a C to G substitution at nucleotide position 1062, causing the aspartic acid (D) at amino acid position 354 to be replaced by a glutamic acid (E). 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