3-46021146-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001024644.2(XCR1):c.802G>A(p.Ala268Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001024644.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XCR1 | NM_001024644.2 | c.802G>A | p.Ala268Thr | missense_variant | Exon 2 of 2 | ENST00000309285.4 | NP_001019815.1 | |
XCR1 | NM_001381860.1 | c.802G>A | p.Ala268Thr | missense_variant | Exon 4 of 4 | NP_001368789.1 | ||
XCR1 | NM_005283.3 | c.802G>A | p.Ala268Thr | 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.802G>A | p.Ala268Thr | missense_variant | Exon 2 of 2 | 1 | NM_001024644.2 | ENSP00000310405.3 | ||
XCR1 | ENST00000395946.3 | c.802G>A | p.Ala268Thr | missense_variant | Exon 3 of 3 | 1 | ENSP00000379277.3 | |||
XCR1 | ENST00000683768.1 | c.802G>A | p.Ala268Thr | missense_variant | Exon 6 of 6 | ENSP00000507745.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461890Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.802G>A (p.A268T) 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 802, causing the alanine (A) at amino acid position 268 to be replaced by a threonine (T). 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