7-75771960-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001371938.1(CCL26):c.117C>A(p.His39Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001371938.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL26 | NM_001371938.1 | c.117C>A | p.His39Gln | missense_variant | 2/3 | ENST00000005180.9 | |
CCL26 | NM_001371936.1 | c.117C>A | p.His39Gln | missense_variant | 3/4 | ||
CCL26 | NM_006072.4 | c.117C>A | p.His39Gln | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL26 | ENST00000005180.9 | c.117C>A | p.His39Gln | missense_variant | 2/3 | 1 | NM_001371938.1 | P1 | |
CCL26 | ENST00000394905.2 | c.117C>A | p.His39Gln | missense_variant | 3/4 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461836Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727234
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.117C>A (p.H39Q) alteration is located in exon 3 (coding exon 2) of the CCL26 gene. This alteration results from a C to A substitution at nucleotide position 117, causing the histidine (H) at amino acid position 39 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