chr2-239053470-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001378414.1(HDAC4):c.3220G>A(p.Ala1074Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000567 in 1,612,938 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001378414.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC4 | NM_001378414.1 | c.3220G>A | p.Ala1074Thr | missense_variant | Exon 26 of 27 | ENST00000543185.6 | NP_001365343.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC4 | ENST00000543185.6 | c.3220G>A | p.Ala1074Thr | missense_variant | Exon 26 of 27 | 5 | NM_001378414.1 | ENSP00000440481.3 | ||
HDAC4 | ENST00000345617.7 | c.3205G>A | p.Ala1069Thr | missense_variant | Exon 26 of 27 | 1 | ENSP00000264606.3 | |||
HDAC4 | ENST00000430200.1 | c.475G>A | p.Ala159Thr | missense_variant | Exon 3 of 4 | 3 | ENSP00000410551.1 | |||
HDAC4 | ENST00000690129.1 | n.1234G>A | non_coding_transcript_exon_variant | Exon 9 of 10 |
Frequencies
GnomAD3 genomes AF: 0.000434 AC: 66AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000564 AC: 141AN: 249986Hom.: 1 AF XY: 0.000576 AC XY: 78AN XY: 135318
GnomAD4 exome AF: 0.000581 AC: 848AN: 1460596Hom.: 2 Cov.: 32 AF XY: 0.000603 AC XY: 438AN XY: 726528
GnomAD4 genome AF: 0.000433 AC: 66AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74486
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at