chr3-46021707-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001024644.2(XCR1):c.241G>C(p.Ala81Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A81T) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XCR1 | NM_001024644.2 | c.241G>C | p.Ala81Pro | missense_variant | 2/2 | ENST00000309285.4 | |
XCR1 | NM_001381860.1 | c.241G>C | p.Ala81Pro | missense_variant | 4/4 | ||
XCR1 | NM_005283.3 | c.241G>C | p.Ala81Pro | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XCR1 | ENST00000309285.4 | c.241G>C | p.Ala81Pro | missense_variant | 2/2 | 1 | NM_001024644.2 | P1 | |
XCR1 | ENST00000395946.3 | c.241G>C | p.Ala81Pro | missense_variant | 3/3 | 1 | P1 | ||
XCR1 | ENST00000683768.1 | c.241G>C | p.Ala81Pro | missense_variant | 6/6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2023 | The c.241G>C (p.A81P) alteration is located in exon 3 (coding exon 1) of the XCR1 gene. This alteration results from a G to C substitution at nucleotide position 241, causing the alanine (A) at amino acid position 81 to be replaced by a proline (P). 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
Publications
No publications associated with this variant yet.