3-149041495-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003071.4(HLTF):c.2371G>A(p.Glu791Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,611,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003071.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HLTF | NM_003071.4 | c.2371G>A | p.Glu791Lys | missense_variant | Exon 20 of 25 | ENST00000310053.10 | NP_003062.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250182Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135224
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459614Hom.: 0 Cov.: 29 AF XY: 0.00000551 AC XY: 4AN XY: 726056
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2371G>A (p.E791K) alteration is located in exon 20 (coding exon 20) of the HLTF gene. This alteration results from a G to A substitution at nucleotide position 2371, causing the glutamic acid (E) at amino acid position 791 to be replaced by a lysine (K). 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