chr3-149042174-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003071.4(HLTF):c.2189G>A(p.Gly730Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,612,796 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003071.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HLTF | NM_003071.4 | c.2189G>A | p.Gly730Asp | missense_variant | Exon 19 of 25 | ENST00000310053.10 | NP_003062.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000855 AC: 130AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000753 AC: 189AN: 251130Hom.: 0 AF XY: 0.000751 AC XY: 102AN XY: 135734
GnomAD4 exome AF: 0.00123 AC: 1799AN: 1460652Hom.: 2 Cov.: 30 AF XY: 0.00119 AC XY: 865AN XY: 726664
GnomAD4 genome AF: 0.000848 AC: 129AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000807 AC XY: 60AN XY: 74368
ClinVar
Submissions by phenotype
HLTF-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at