16-57382093-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_002996.6(CX3CL1):āc.255G>Cā(p.Ala85Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002996.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CX3CL1 | ENST00000006053.7 | c.255G>C | p.Ala85Ala | synonymous_variant | Exon 3 of 3 | 1 | NM_002996.6 | ENSP00000006053.6 | ||
CX3CL1 | ENST00000565912.1 | c.141G>C | p.Ala47Ala | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000464114.1 | |||
CX3CL1 | ENST00000564948.1 | c.134G>C | p.Arg45Pro | missense_variant | Exon 2 of 2 | 3 | ENSP00000457996.1 | |||
CX3CL1 | ENST00000563383.1 | c.273G>C | p.Ala91Ala | synonymous_variant | Exon 3 of 3 | 5 | ENSP00000456830.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461430Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726956
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at