17-36013826-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005064.6(CCL23):c.220T>A(p.Ser74Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 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. S74P) has been classified as Uncertain significance.
Frequency
Consequence
NM_005064.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL23 | NM_005064.6 | c.220T>A | p.Ser74Thr | missense_variant | 3/4 | ENST00000615050.2 | |
CCL23 | NM_145898.4 | c.169T>A | p.Ser57Thr | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL23 | ENST00000615050.2 | c.220T>A | p.Ser74Thr | missense_variant | 3/4 | 1 | NM_005064.6 | P2 | |
CCL23 | ENST00000612516.4 | c.169T>A | p.Ser57Thr | missense_variant | 3/4 | 1 | A2 | ||
CCL23 | ENST00000613876.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251466Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135910
GnomAD4 exome AF: 0.000187 AC: 273AN: 1461822Hom.: 0 Cov.: 32 AF XY: 0.000186 AC XY: 135AN XY: 727214
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.220T>A (p.S74T) alteration is located in exon 3 (coding exon 3) of the CCL23 gene. This alteration results from a T to A substitution at nucleotide position 220, causing the serine (S) at amino acid position 74 to be replaced by a threonine (T). 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