16-57360506-G-A
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4
The NM_002990.5(CCL22):c.143G>A(p.Arg48His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. R48C) has been classified as Uncertain significance.
Frequency
Consequence
NM_002990.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -1 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CCL22 | NM_002990.5 | c.143G>A | p.Arg48His | missense_variant | Exon 2 of 3 | ENST00000219235.5 | NP_002981.2 | |
| CCL22 | XM_047434449.1 | c.182G>A | p.Arg61His | missense_variant | Exon 3 of 4 | XP_047290405.1 | ||
| CCL22 | XM_047434450.1 | c.143G>A | p.Arg48His | missense_variant | Exon 3 of 4 | XP_047290406.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CCL22 | ENST00000219235.5 | c.143G>A | p.Arg48His | missense_variant | Exon 2 of 3 | 1 | NM_002990.5 | ENSP00000219235.4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000676 AC: 17AN: 251468 AF XY: 0.0000809 show subpopulations
GnomAD4 exome AF: 0.000153 AC: 224AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.000131 AC XY: 95AN XY: 727232 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74382 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.143G>A (p.R48H) alteration is located in exon 2 (coding exon 2) of the CCL22 gene. This alteration results from a G to A substitution at nucleotide position 143, causing the arginine (R) at amino acid position 48 to be replaced by a histidine (H). 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