chr17-44078636-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_005474.5(HDAC5):c.3193G>A(p.Ala1065Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,605,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDAC5 | NM_005474.5 | c.3193G>A | p.Ala1065Thr | missense_variant | 26/27 | ENST00000682912.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC5 | ENST00000682912.1 | c.3193G>A | p.Ala1065Thr | missense_variant | 26/27 | NM_005474.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000490 AC: 12AN: 244678Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132798
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1453650Hom.: 0 Cov.: 32 AF XY: 0.0000180 AC XY: 13AN XY: 723402
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.3196G>A (p.A1066T) alteration is located in exon 26 (coding exon 25) of the HDAC5 gene. This alteration results from a G to A substitution at nucleotide position 3196, causing the alanine (A) at amino acid position 1066 to be replaced by a threonine (T). 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