2-227816374-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004591.3(CCL20):c.259C>T(p.Arg87Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000942 in 1,591,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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. R87H) has been classified as Likely benign.
Frequency
Consequence
NM_004591.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCL20 | ENST00000358813.5 | c.259C>T | p.Arg87Cys | missense_variant | Exon 3 of 4 | 1 | NM_004591.3 | ENSP00000351671.4 | ||
CCL20 | ENST00000409189.7 | c.256C>T | p.Arg86Cys | missense_variant | Exon 3 of 4 | 1 | ENSP00000386273.3 | |||
CCL20 | ENST00000473642.1 | n.268C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152106Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249374Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134832
GnomAD4 exome AF: 0.00000695 AC: 10AN: 1439734Hom.: 0 Cov.: 26 AF XY: 0.00000279 AC XY: 2AN XY: 717640
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152106Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.259C>T (p.R87C) alteration is located in exon 3 (coding exon 3) of the CCL20 gene. This alteration results from a C to T substitution at nucleotide position 259, causing the arginine (R) at amino acid position 87 to be replaced by a cysteine (C). 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