6-113958760-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001527.4(HDAC2):c.172C>T(p.His58Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000705 in 1,418,566 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001527.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC2 | NM_001527.4 | c.172C>T | p.His58Tyr | missense_variant | Exon 3 of 14 | ENST00000519065.6 | NP_001518.3 | |
HDAC2 | XM_047418692.1 | c.82C>T | p.His28Tyr | missense_variant | Exon 3 of 14 | XP_047274648.1 | ||
HDAC2 | NR_033441.2 | n.440C>T | non_coding_transcript_exon_variant | Exon 4 of 15 | ||||
HDAC2 | NR_073443.2 | n.370C>T | non_coding_transcript_exon_variant | Exon 3 of 14 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248068Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134586
GnomAD4 exome AF: 7.05e-7 AC: 1AN: 1418566Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 708728
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.172C>T (p.H58Y) alteration is located in exon 3 (coding exon 3) of the HDAC2 gene. This alteration results from a C to T substitution at nucleotide position 172, causing the histidine (H) at amino acid position 58 to be replaced by a tyrosine (Y). 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