chr17-44083611-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_005474.5(HDAC5):c.2397T>G(p.Ser799Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,046 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. S799G) has been classified as Uncertain significance.
Frequency
Consequence
NM_005474.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDAC5 | NM_005474.5 | c.2397T>G | p.Ser799Arg | missense_variant | 18/27 | ENST00000682912.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC5 | ENST00000682912.1 | c.2397T>G | p.Ser799Arg | missense_variant | 18/27 | NM_005474.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250848Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135682
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461792Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727190
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.2400T>G (p.S800R) alteration is located in exon 18 (coding exon 17) of the HDAC5 gene. This alteration results from a T to G substitution at nucleotide position 2400, causing the serine (S) at amino acid position 800 to be replaced by an arginine (R). 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