chr3-46021914-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001024644.2(XCR1):c.34T>G(p.Phe12Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,728 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_001024644.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XCR1 | NM_001024644.2 | c.34T>G | p.Phe12Val | missense_variant | 2/2 | ENST00000309285.4 | |
XCR1 | NM_001381860.1 | c.34T>G | p.Phe12Val | missense_variant | 4/4 | ||
XCR1 | NM_005283.3 | c.34T>G | p.Phe12Val | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XCR1 | ENST00000309285.4 | c.34T>G | p.Phe12Val | missense_variant | 2/2 | 1 | NM_001024644.2 | P1 | |
XCR1 | ENST00000395946.3 | c.34T>G | p.Phe12Val | missense_variant | 3/3 | 1 | P1 | ||
XCR1 | ENST00000683768.1 | c.34T>G | p.Phe12Val | missense_variant | 6/6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250508Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135324
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461582Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727102
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.34T>G (p.F12V) alteration is located in exon 3 (coding exon 1) of the XCR1 gene. This alteration results from a T to G substitution at nucleotide position 34, causing the phenylalanine (F) at amino acid position 12 to be replaced by a valine (V). 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