3-46021076-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001024644.2(XCR1):c.872G>A(p.Gly291Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,614,112 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G291R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001024644.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XCR1 | NM_001024644.2 | c.872G>A | p.Gly291Glu | missense_variant | Exon 2 of 2 | ENST00000309285.4 | NP_001019815.1 | |
XCR1 | NM_001381860.1 | c.872G>A | p.Gly291Glu | missense_variant | Exon 4 of 4 | NP_001368789.1 | ||
XCR1 | NM_005283.3 | c.872G>A | p.Gly291Glu | missense_variant | Exon 3 of 3 | NP_005274.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XCR1 | ENST00000309285.4 | c.872G>A | p.Gly291Glu | missense_variant | Exon 2 of 2 | 1 | NM_001024644.2 | ENSP00000310405.3 | ||
XCR1 | ENST00000395946.3 | c.872G>A | p.Gly291Glu | missense_variant | Exon 3 of 3 | 1 | ENSP00000379277.3 | |||
XCR1 | ENST00000683768.1 | c.872G>A | p.Gly291Glu | missense_variant | Exon 6 of 6 | ENSP00000507745.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251310Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135842
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461872Hom.: 1 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 727236
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.872G>A (p.G291E) alteration is located in exon 3 (coding exon 1) of the XCR1 gene. This alteration results from a G to A substitution at nucleotide position 872, causing the glycine (G) at amino acid position 291 to be replaced by a glutamic acid (E). 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