rs570367630
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_001375405.1(CEP120):c.2359-8T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000915 in 1,584,302 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001375405.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP120 | NM_001375405.1 | c.2359-8T>A | splice_region_variant, intron_variant | ENST00000306467.10 | NP_001362334.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP120 | ENST00000306467.10 | c.2359-8T>A | splice_region_variant, intron_variant | 5 | NM_001375405.1 | ENSP00000303058.6 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000941 AC: 21AN: 223218Hom.: 0 AF XY: 0.0000581 AC XY: 7AN XY: 120552
GnomAD4 exome AF: 0.0000943 AC: 135AN: 1432106Hom.: 1 Cov.: 28 AF XY: 0.0000842 AC XY: 60AN XY: 712182
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74404
ClinVar
Submissions by phenotype
Short-rib thoracic dysplasia 13 with or without polydactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at