chr1-45500031-G-T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000625766.2(CCDC163):n.-422C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 519,220 control chromosomes in the GnomAD database, including 135,946 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000625766.2 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt | 
|---|---|---|---|---|---|---|---|---|
| CCDC163 | NM_001102601.3 | c.-422C>A | 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>A | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_001102601.3 | ENSP00000486197.1 | 
Frequencies
GnomAD3 genomes  0.738  AC: 112041AN: 151912Hom.:  41753  Cov.: 31 show subpopulations 
GnomAD4 exome  AF:  0.711  AC: 260924AN: 367190Hom.:  94159  Cov.: 2 AF XY:  0.710  AC XY: 137491AN XY: 193660 show subpopulations 
Age Distribution
GnomAD4 genome  0.738  AC: 112131AN: 152030Hom.:  41787  Cov.: 31 AF XY:  0.742  AC XY: 55143AN XY: 74310 show subpopulations 
Age Distribution
ClinVar
Submissions by phenotype
not provided    Benign:2 
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source: 
Splicing
 Find out detailed SpliceAI scores and Pangolin per-transcript scores at