6-113956160-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001527.4(HDAC2):c.359-9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000194 in 1,594,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001527.4 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC2 | NM_001527.4 | c.359-9A>G | intron_variant | Intron 4 of 13 | ENST00000519065.6 | NP_001518.3 | ||
HDAC2 | XM_047418692.1 | c.269-9A>G | intron_variant | Intron 4 of 13 | XP_047274648.1 | |||
HDAC2 | NR_033441.2 | n.627-9A>G | intron_variant | Intron 5 of 14 | ||||
HDAC2 | NR_073443.2 | n.557-9A>G | intron_variant | Intron 4 of 13 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000174 AC: 4AN: 230222Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125084
GnomAD4 exome AF: 0.0000180 AC: 26AN: 1442622Hom.: 0 Cov.: 29 AF XY: 0.0000181 AC XY: 13AN XY: 717286
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74310
ClinVar
Submissions by phenotype
HDAC2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at