rs117083334
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000278935.8(CEP164):āc.1430A>Gā(p.His477Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.033 in 1,609,834 control chromosomes in the GnomAD database, including 1,055 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. H477H) has been classified as Likely benign.
Frequency
Consequence
ENST00000278935.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP164 | NM_014956.5 | c.1430A>G | p.His477Arg | missense_variant | 13/33 | ENST00000278935.8 | NP_055771.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP164 | ENST00000278935.8 | c.1430A>G | p.His477Arg | missense_variant | 13/33 | 1 | NM_014956.5 | ENSP00000278935 | P1 | |
CEP164 | ENST00000533675.5 | n.1685A>G | non_coding_transcript_exon_variant | 9/27 | 2 | |||||
CEP164 | ENST00000533706.5 | n.754A>G | non_coding_transcript_exon_variant | 6/27 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0250 AC: 3805AN: 152122Hom.: 53 Cov.: 32
GnomAD3 exomes AF: 0.0241 AC: 5735AN: 237776Hom.: 106 AF XY: 0.0249 AC XY: 3228AN XY: 129496
GnomAD4 exome AF: 0.0339 AC: 49368AN: 1457594Hom.: 1002 Cov.: 30 AF XY: 0.0335 AC XY: 24248AN XY: 724724
GnomAD4 genome AF: 0.0250 AC: 3804AN: 152240Hom.: 53 Cov.: 32 AF XY: 0.0235 AC XY: 1752AN XY: 74438
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 01, 2015 | - - |
Nephronophthisis 15 Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at