chrX-72351740-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_018486.3(HDAC8):c.1104C>T(p.Tyr368Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000887 in 112,723 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018486.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC8 | ENST00000373573.9 | c.1104C>T | p.Tyr368Tyr | synonymous_variant | Exon 10 of 11 | 1 | NM_018486.3 | ENSP00000362674.3 | ||
ENSG00000285547 | ENST00000648922.1 | c.1104C>T | p.Tyr368Tyr | synonymous_variant | Exon 10 of 12 | ENSP00000497072.1 |
Frequencies
GnomAD3 genomes AF: 0.00000887 AC: 1AN: 112723Hom.: 0 Cov.: 23 AF XY: 0.0000287 AC XY: 1AN XY: 34859
GnomAD4 exome Cov.: 27
GnomAD4 genome AF: 0.00000887 AC: 1AN: 112723Hom.: 0 Cov.: 23 AF XY: 0.0000287 AC XY: 1AN XY: 34859
ClinVar
Submissions by phenotype
Cornelia de Lange syndrome 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at