1-45500031-G-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001102601.3(CCDC163):c.-422C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001102601.3 5_prime_UTR
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC163 | NM_001102601.3 | c.-422C>G | 5_prime_UTR_variant | Exon 1 of 5 | ENST00000629482.3 | NP_001096071.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC163 | ENST00000629482.3 | c.-422C>G | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_001102601.3 | ENSP00000486197.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151962Hom.: 0 Cov.: 31 show subpopulations
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000272 AC: 1AN: 367720Hom.: 0 Cov.: 2 AF XY: 0.00000516 AC XY: 1AN XY: 193946 show subpopulations
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151962Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74204 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at