rs61744334
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001375405.1(CEP120):āc.2182A>Gā(p.Ser728Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 1,606,672 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001375405.1 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 |
---|---|---|---|---|---|---|---|
CEP120 | NM_001375405.1 | c.2182A>G | p.Ser728Gly | missense_variant | 15/20 | ENST00000306467.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP120 | ENST00000306467.10 | c.2182A>G | p.Ser728Gly | missense_variant | 15/20 | 5 | NM_001375405.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00692 AC: 1050AN: 151688Hom.: 9 Cov.: 30
GnomAD3 exomes AF: 0.00186 AC: 456AN: 245084Hom.: 7 AF XY: 0.00134 AC XY: 178AN XY: 132690
GnomAD4 exome AF: 0.000782 AC: 1138AN: 1454864Hom.: 9 Cov.: 31 AF XY: 0.000734 AC XY: 531AN XY: 723886
GnomAD4 genome AF: 0.00704 AC: 1069AN: 151808Hom.: 10 Cov.: 30 AF XY: 0.00747 AC XY: 554AN XY: 74184
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | May 10, 2022 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 05, 2020 | - - |
Short-rib thoracic dysplasia 13 with or without polydactyly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at