16-57358823-C-T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002990.5(CCL22):c.7C>T(p.Arg3Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,460,574 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_002990.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CCL22 | NM_002990.5 | c.7C>T | p.Arg3Cys | missense_variant | Exon 1 of 3 | ENST00000219235.5 | NP_002981.2 | |
| CCL22 | XM_047434449.1 | c.46C>T | p.Arg16Cys | missense_variant | Exon 2 of 4 | XP_047290405.1 | ||
| CCL22 | XM_047434450.1 | c.7C>T | p.Arg3Cys | missense_variant | Exon 2 of 4 | XP_047290406.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CCL22 | ENST00000219235.5 | c.7C>T | p.Arg3Cys | missense_variant | Exon 1 of 3 | 1 | NM_002990.5 | ENSP00000219235.4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251432 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460574Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726662 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.7C>T (p.R3C) alteration is located in exon 1 (coding exon 1) of the CCL22 gene. This alteration results from a C to T substitution at nucleotide position 7, causing the arginine (R) at amino acid position 3 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