chr1-180787774-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP2BP4
The NM_004736.4(XPR1):c.143A>G(p.Lys48Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004736.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPR1 | NM_004736.4 | c.143A>G | p.Lys48Arg | missense_variant | 3/15 | ENST00000367590.9 | |
XPR1 | NM_001135669.2 | c.143A>G | p.Lys48Arg | missense_variant | 3/14 | ||
XPR1 | NM_001328662.2 | c.143A>G | p.Lys48Arg | missense_variant | 3/11 | ||
XPR1 | NR_137330.2 | n.323A>G | non_coding_transcript_exon_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPR1 | ENST00000367590.9 | c.143A>G | p.Lys48Arg | missense_variant | 3/15 | 1 | NM_004736.4 | P1 | |
XPR1 | ENST00000367589.3 | c.143A>G | p.Lys48Arg | missense_variant | 3/14 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460606Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726618
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 05, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.