2-233841177-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018410.5(HJURP):c.1603C>T(p.Arg535Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018410.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HJURP | ENST00000411486.7 | c.1603C>T | p.Arg535Cys | missense_variant | 8/9 | 1 | NM_018410.5 | ENSP00000414109.1 | ||
HJURP | ENST00000432087.5 | c.1441C>T | p.Arg481Cys | missense_variant | 6/7 | 2 | ENSP00000407208.1 | |||
HJURP | ENST00000441687.5 | c.1348C>T | p.Arg450Cys | missense_variant | 5/6 | 2 | ENSP00000401944.1 | |||
HJURP | ENST00000414924.5 | c.1348C>T | p.Arg450Cys | missense_variant | 5/5 | 4 | ENSP00000393253.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251476Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135912
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461886Hom.: 0 Cov.: 35 AF XY: 0.0000165 AC XY: 12AN XY: 727244
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.1603C>T (p.R535C) alteration is located in exon 8 (coding exon 8) of the HJURP gene. This alteration results from a C to T substitution at nucleotide position 1603, causing the arginine (R) at amino acid position 535 to be replaced by a cysteine (C). 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