chr6-167136379-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_031409.4(CCR6):c.149C>T(p.Pro50Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000547 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P50P) has been classified as Likely benign.
Frequency
Consequence
NM_031409.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCR6 | NM_031409.4 | c.149C>T | p.Pro50Leu | missense_variant | 3/3 | ENST00000341935.10 | |
CCR6 | NM_001394582.1 | c.149C>T | p.Pro50Leu | missense_variant | 4/4 | ||
CCR6 | NM_004367.6 | c.149C>T | p.Pro50Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR6 | ENST00000341935.10 | c.149C>T | p.Pro50Leu | missense_variant | 3/3 | 1 | NM_031409.4 | P1 | |
CCR6 | ENST00000349984.6 | c.149C>T | p.Pro50Leu | missense_variant | 4/4 | 1 | P1 | ||
CCR6 | ENST00000400926.5 | c.149C>T | p.Pro50Leu | missense_variant | 3/3 | 2 | P1 | ||
CCR6 | ENST00000643861.1 | c.149C>T | p.Pro50Leu | missense_variant | 4/4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251208Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135754
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461862Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727232
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.149C>T (p.P50L) alteration is located in exon 3 (coding exon 2) of the CCR6 gene. This alteration results from a C to T substitution at nucleotide position 149, causing the proline (P) at amino acid position 50 to be replaced by a leucine (L). 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