rs763500364
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PP5_ModerateBP4BS2_Supporting
The NM_001395891.1(CLASP1):c.196-665C>T variant causes a intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 700,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_001395891.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLASP1 | NM_001395891.1 | c.196-665C>T | intron_variant | Intron 2 of 40 | ENST00000696935.1 | NP_001382820.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLASP1 | ENST00000696935.1 | c.196-665C>T | intron_variant | Intron 2 of 40 | NM_001395891.1 | ENSP00000512981.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000383 AC: 5AN: 130490Hom.: 0 AF XY: 0.0000140 AC XY: 1AN XY: 71230
GnomAD4 exome AF: 0.0000128 AC: 7AN: 548024Hom.: 0 Cov.: 0 AF XY: 0.00000674 AC XY: 2AN XY: 296754
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74246
ClinVar
Submissions by phenotype
Lowry-Wood syndrome Pathogenic:1
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not provided Pathogenic:1
This variant occurs in the RNU4ATAC gene, which encodes an RNA molecule that does not result in a protein product. This variant is present in population databases (rs763500364, gnomAD 0.02%). This variant has been observed in individual(s) with RNU4ATAC-related conditions (PMID: 21474760, 29265708; internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 30181). Functional studies have shown that this variant disrupts ncRNA function (PMID: 21474760, 32628740) For these reasons, this variant has been classified as Pathogenic. -
Osteodysplastic primordial dwarfism, type 1 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at