16-57415102-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002987.3(CCL17):c.92G>A(p.Arg31Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002987.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCL17 | NM_002987.3 | c.92G>A | p.Arg31Gln | missense_variant | 3/4 | ENST00000219244.9 | NP_002978.1 | |
CCL17 | XM_017023530.2 | c.179G>A | p.Arg60Gln | missense_variant | 5/6 | XP_016879019.1 | ||
CCL17 | XM_011523256.3 | c.176G>A | p.Arg59Gln | missense_variant | 5/6 | XP_011521558.1 | ||
CCL17 | XM_047434448.1 | c.92G>A | p.Arg31Gln | missense_variant | 2/3 | XP_047290404.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCL17 | ENST00000219244.9 | c.92G>A | p.Arg31Gln | missense_variant | 3/4 | 1 | NM_002987.3 | ENSP00000219244.4 | ||
CCL17 | ENST00000616880.1 | c.92G>A | p.Arg31Gln | missense_variant | 2/3 | 1 | ENSP00000480147.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251388Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135882
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461380Hom.: 0 Cov.: 31 AF XY: 0.0000481 AC XY: 35AN XY: 727060
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.92G>A (p.R31Q) alteration is located in exon 3 (coding exon 2) of the CCL17 gene. This alteration results from a G to A substitution at nucleotide position 92, causing the arginine (R) at amino acid position 31 to be replaced by a glutamine (Q). 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