chr3-46021040-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001024644.2(XCR1):c.908G>A(p.Arg303Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,613,994 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001024644.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XCR1 | NM_001024644.2 | c.908G>A | p.Arg303Gln | missense_variant | 2/2 | ENST00000309285.4 | |
XCR1 | NM_001381860.1 | c.908G>A | p.Arg303Gln | missense_variant | 4/4 | ||
XCR1 | NM_005283.3 | c.908G>A | p.Arg303Gln | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XCR1 | ENST00000309285.4 | c.908G>A | p.Arg303Gln | missense_variant | 2/2 | 1 | NM_001024644.2 | P1 | |
XCR1 | ENST00000395946.3 | c.908G>A | p.Arg303Gln | missense_variant | 3/3 | 1 | P1 | ||
XCR1 | ENST00000683768.1 | c.908G>A | p.Arg303Gln | missense_variant | 6/6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000958 AC: 24AN: 250492Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135472
GnomAD4 exome AF: 0.000101 AC: 148AN: 1461658Hom.: 2 Cov.: 30 AF XY: 0.000120 AC XY: 87AN XY: 727116
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74496
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at