7-75771934-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001371938.1(CCL26):c.143G>A(p.Arg48Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,614,014 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 Likely benign (★).
Frequency
Consequence
NM_001371938.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL26 | NM_001371938.1 | c.143G>A | p.Arg48Gln | missense_variant | 2/3 | ENST00000005180.9 | |
CCL26 | NM_001371936.1 | c.143G>A | p.Arg48Gln | missense_variant | 3/4 | ||
CCL26 | NM_006072.4 | c.143G>A | p.Arg48Gln | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL26 | ENST00000005180.9 | c.143G>A | p.Arg48Gln | missense_variant | 2/3 | 1 | NM_001371938.1 | P1 | |
CCL26 | ENST00000394905.2 | c.143G>A | p.Arg48Gln | missense_variant | 3/4 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251432Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135878
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461760Hom.: 0 Cov.: 30 AF XY: 0.0000509 AC XY: 37AN XY: 727192
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at