6-113943462-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001527.4(HDAC2):c.1267G>A(p.Asp423Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,609,542 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC2 | NM_001527.4 | c.1267G>A | p.Asp423Asn | missense_variant | Exon 12 of 14 | ENST00000519065.6 | NP_001518.3 | |
HDAC2 | XM_047418692.1 | c.1177G>A | p.Asp393Asn | missense_variant | Exon 12 of 14 | XP_047274648.1 | ||
HDAC2 | NR_033441.2 | n.1535G>A | non_coding_transcript_exon_variant | Exon 13 of 15 | ||||
HDAC2 | NR_073443.2 | n.1465G>A | non_coding_transcript_exon_variant | Exon 12 of 14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC2 | ENST00000519065.6 | c.1267G>A | p.Asp423Asn | missense_variant | Exon 12 of 14 | 1 | NM_001527.4 | ENSP00000430432.1 | ||
HDAC2 | ENST00000368632.6 | c.1177G>A | p.Asp393Asn | missense_variant | Exon 13 of 15 | 2 | ENSP00000357621.2 | |||
HDAC2 | ENST00000519108.5 | c.1177G>A | p.Asp393Asn | missense_variant | Exon 12 of 14 | 2 | ENSP00000430008.1 | |||
HDAC2 | ENST00000523334.1 | n.4270G>A | non_coding_transcript_exon_variant | Exon 6 of 8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246138Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133816
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1457342Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3AN XY: 725212
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1267G>A (p.D423N) alteration is located in exon 12 (coding exon 12) of the HDAC2 gene. This alteration results from a G to A substitution at nucleotide position 1267, causing the aspartic acid (D) at amino acid position 423 to be replaced by an asparagine (N). 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