12-47787745-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_015401.5(HDAC7):c.2420C>A(p.Pro807His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000701 in 1,612,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. P807A) has been classified as Uncertain significance.
Frequency
Consequence
NM_015401.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDAC7 | NM_015401.5 | c.2420C>A | p.Pro807His | missense_variant | 21/26 | ENST00000080059.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC7 | ENST00000080059.12 | c.2420C>A | p.Pro807His | missense_variant | 21/26 | 1 | NM_015401.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 151958Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000446 AC: 11AN: 246738Hom.: 0 AF XY: 0.0000598 AC XY: 8AN XY: 133812
GnomAD4 exome AF: 0.0000678 AC: 99AN: 1460184Hom.: 0 Cov.: 31 AF XY: 0.0000812 AC XY: 59AN XY: 726250
GnomAD4 genome ? AF: 0.0000921 AC: 14AN: 151958Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74220
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.2420C>A (p.P807H) alteration is located in exon 21 (coding exon 21) of the HDAC7 gene. This alteration results from a C to A substitution at nucleotide position 2420, causing the proline (P) at amino acid position 807 to be replaced by a histidine (H). 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