chr7-130400746-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_018718.3(CEP41):c.718T>G(p.Cys240Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,613,780 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. C240C) has been classified as Likely benign.
Frequency
Consequence
NM_018718.3 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 | UniProt |
---|---|---|---|---|---|---|---|
CEP41 | NM_018718.3 | c.718T>G | p.Cys240Gly | missense_variant | 9/11 | ENST00000223208.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP41 | ENST00000223208.10 | c.718T>G | p.Cys240Gly | missense_variant | 9/11 | 1 | NM_018718.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00693 AC: 1055AN: 152206Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00166 AC: 417AN: 250872Hom.: 5 AF XY: 0.00111 AC XY: 150AN XY: 135558
GnomAD4 exome AF: 0.000738 AC: 1079AN: 1461456Hom.: 16 Cov.: 30 AF XY: 0.000659 AC XY: 479AN XY: 726994
GnomAD4 genome ? AF: 0.00693 AC: 1056AN: 152324Hom.: 10 Cov.: 32 AF XY: 0.00615 AC XY: 458AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 18, 2018 | 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 10, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | CEP41: BS1, BS2 - |
Joubert syndrome 15 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 08, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at