6-113944342-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001527.4(HDAC2):āc.1160A>Gā(p.Glu387Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,036 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001527.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC2 | NM_001527.4 | c.1160A>G | p.Glu387Gly | missense_variant | Exon 11 of 14 | ENST00000519065.6 | NP_001518.3 | |
HDAC2 | XM_047418692.1 | c.1070A>G | p.Glu357Gly | missense_variant | Exon 11 of 14 | XP_047274648.1 | ||
HDAC2 | NR_033441.2 | n.1428A>G | non_coding_transcript_exon_variant | Exon 12 of 15 | ||||
HDAC2 | NR_073443.2 | n.1358A>G | non_coding_transcript_exon_variant | Exon 11 of 14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC2 | ENST00000519065.6 | c.1160A>G | p.Glu387Gly | missense_variant | Exon 11 of 14 | 1 | NM_001527.4 | ENSP00000430432.1 | ||
HDAC2 | ENST00000368632.6 | c.1070A>G | p.Glu357Gly | missense_variant | Exon 12 of 15 | 2 | ENSP00000357621.2 | |||
HDAC2 | ENST00000519108.5 | c.1070A>G | p.Glu357Gly | missense_variant | Exon 11 of 14 | 2 | ENSP00000430008.1 | |||
HDAC2 | ENST00000523334.1 | n.4163A>G | non_coding_transcript_exon_variant | Exon 5 of 8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460844Hom.: 0 Cov.: 29 AF XY: 0.0000138 AC XY: 10AN XY: 726820
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1160A>G (p.E387G) alteration is located in exon 11 (coding exon 11) of the HDAC2 gene. This alteration results from a A to G substitution at nucleotide position 1160, causing the glutamic acid (E) at amino acid position 387 to be replaced by a glycine (G). 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