X-84440548-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001177479.2(HDX):c.1289G>T(p.Cys430Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000288 in 1,181,118 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001177479.2 missense
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 |
---|---|---|---|---|---|---|---|---|---|---|
HDX | ENST00000373177.3 | c.1289G>T | p.Cys430Phe | missense_variant | Exon 5 of 11 | 1 | NM_001177479.2 | ENSP00000362272.2 | ||
HDX | ENST00000297977.9 | c.1289G>T | p.Cys430Phe | missense_variant | Exon 4 of 10 | 1 | ENSP00000297977.5 | |||
HDX | ENST00000506585.6 | c.1115G>T | p.Cys372Phe | missense_variant | Exon 4 of 10 | 2 | ENSP00000423670.2 | |||
HDX | ENST00000472135.2 | n.1143G>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000990 AC: 11AN: 111103Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33445
GnomAD3 exomes AF: 0.0000171 AC: 3AN: 175663Hom.: 0 AF XY: 0.0000164 AC XY: 1AN XY: 61111
GnomAD4 exome AF: 0.0000215 AC: 23AN: 1070015Hom.: 0 Cov.: 24 AF XY: 0.0000176 AC XY: 6AN XY: 340685
GnomAD4 genome AF: 0.0000990 AC: 11AN: 111103Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33445
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1289G>T (p.C430F) alteration is located in exon 5 (coding exon 3) of the HDX gene. This alteration results from a G to T substitution at nucleotide position 1289, causing the cysteine (C) at amino acid position 430 to be replaced by a phenylalanine (F). 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