chr16-57382344-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002996.6(CX3CL1):c.506T>C(p.Leu169Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000999 in 1,601,720 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_002996.6 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 |
---|---|---|---|---|---|---|---|
CX3CL1 | NM_002996.6 | c.506T>C | p.Leu169Pro | missense_variant | 3/3 | ENST00000006053.7 | |
CX3CL1 | NM_001304392.3 | c.251T>C | p.Leu84Pro | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CX3CL1 | ENST00000006053.7 | c.506T>C | p.Leu169Pro | missense_variant | 3/3 | 1 | NM_002996.6 | P4 | |
CX3CL1 | ENST00000565912.1 | c.392T>C | p.Leu131Pro | missense_variant | 2/2 | 1 | |||
CX3CL1 | ENST00000563383.1 | c.524T>C | p.Leu175Pro | missense_variant | 3/3 | 5 | A2 | ||
CX3CL1 | ENST00000564948.1 | c.*217T>C | 3_prime_UTR_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000660 AC: 10AN: 151434Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000826 AC: 2AN: 242012Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131992
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1450286Hom.: 0 Cov.: 31 AF XY: 0.00000555 AC XY: 4AN XY: 721182
GnomAD4 genome ? AF: 0.0000660 AC: 10AN: 151434Hom.: 0 Cov.: 31 AF XY: 0.0000947 AC XY: 7AN XY: 73922
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.506T>C (p.L169P) alteration is located in exon 3 (coding exon 3) of the CX3CL1 gene. This alteration results from a T to C substitution at nucleotide position 506, causing the leucine (L) at amino acid position 169 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