chr17-44078621-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_005474.5(HDAC5):c.3208C>T(p.Arg1070Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,607,132 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDAC5 | NM_005474.5 | c.3208C>T | p.Arg1070Trp | missense_variant | 26/27 | ENST00000682912.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC5 | ENST00000682912.1 | c.3208C>T | p.Arg1070Trp | missense_variant | 26/27 | NM_005474.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000936 AC: 23AN: 245632Hom.: 0 AF XY: 0.000105 AC XY: 14AN XY: 133366
GnomAD4 exome AF: 0.000153 AC: 222AN: 1454972Hom.: 1 Cov.: 32 AF XY: 0.000134 AC XY: 97AN XY: 724146
GnomAD4 genome AF: 0.000125 AC: 19AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.3211C>T (p.R1071W) alteration is located in exon 26 (coding exon 25) of the HDAC5 gene. This alteration results from a C to T substitution at nucleotide position 3211, causing the arginine (R) at amino acid position 1071 to be replaced by a tryptophan (W). 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