rs13204445
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001527.4(HDAC2):c.1092-13A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001527.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDAC2 | NM_001527.4 | c.1092-13A>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000519065.6 | |||
HDAC2 | XM_047418692.1 | c.1002-13A>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
HDAC2 | NR_033441.2 | n.1360-13A>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
HDAC2 | NR_073443.2 | n.1290-13A>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC2 | ENST00000519065.6 | c.1092-13A>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001527.4 | P1 | |||
HDAC2 | ENST00000368632.6 | c.1002-13A>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
HDAC2 | ENST00000519108.5 | c.1002-13A>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
HDAC2 | ENST00000523334.1 | n.4095-13A>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152042Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74266
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at