chr17-44087517-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_005474.5(HDAC5):āc.1779C>Gā(p.Asp593Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 1,610,846 control chromosomes in the GnomAD database, including 451,156 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_005474.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDAC5 | NM_005474.5 | c.1779C>G | p.Asp593Glu | missense_variant | 13/27 | ENST00000682912.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC5 | ENST00000682912.1 | c.1779C>G | p.Asp593Glu | missense_variant | 13/27 | NM_005474.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.709 AC: 107715AN: 151858Hom.: 38766 Cov.: 31
GnomAD3 exomes AF: 0.767 AC: 192349AN: 250930Hom.: 74431 AF XY: 0.770 AC XY: 104514AN XY: 135670
GnomAD4 exome AF: 0.750 AC: 1094459AN: 1458872Hom.: 412358 Cov.: 34 AF XY: 0.753 AC XY: 546780AN XY: 725902
GnomAD4 genome AF: 0.709 AC: 107796AN: 151974Hom.: 38798 Cov.: 31 AF XY: 0.717 AC XY: 53263AN XY: 74278
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 13, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at