chr17-44078413-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_005474.5(HDAC5):c.3332C>T(p.Pro1111Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000913 in 1,533,496 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005474.5 missense, splice_region
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.3332C>T | p.Pro1111Leu | missense_variant, splice_region_variant | 27/27 | ENST00000682912.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC5 | ENST00000682912.1 | c.3332C>T | p.Pro1111Leu | missense_variant, splice_region_variant | 27/27 | NM_005474.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000261 AC: 5AN: 191692Hom.: 0 AF XY: 0.0000391 AC XY: 4AN XY: 102418
GnomAD4 exome AF: 0.00000796 AC: 11AN: 1381274Hom.: 0 Cov.: 31 AF XY: 0.00000885 AC XY: 6AN XY: 678266
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.3335C>T (p.P1112L) alteration is located in exon 27 (coding exon 26) of the HDAC5 gene. This alteration results from a C to T substitution at nucleotide position 3335, causing the proline (P) at amino acid position 1112 to be replaced by a leucine (L). 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