2-121530997-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP5BP4BS2_Supporting
The NM_001395891.1(CLASP1):c.196-672A>G variant causes a intron change. The variant allele was found at a frequency of 0.0000443 in 700,202 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001395891.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLASP1 | NM_001395891.1 | c.196-672A>G | 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.196-672A>G | intron_variant | Intron 2 of 40 | NM_001395891.1 | ENSP00000512981.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000230 AC: 3AN: 130486Hom.: 0 AF XY: 0.0000140 AC XY: 1AN XY: 71226
GnomAD4 exome AF: 0.0000511 AC: 28AN: 548044Hom.: 0 Cov.: 0 AF XY: 0.0000371 AC XY: 11AN XY: 296764
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74320
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain: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 (no rsID available, gnomAD 0.008%). This variant has been observed in individual(s) with Roifman syndrome (PMID: 26522830). ClinVar contains an entry for this variant (Variation ID: 218087). This variant is located within the Sm protein-binding region of the RNU4ATAC RNA, which is important for small nuclear RNA maturation (PMID: 32628740). A significant number of disease-associated RNU4ATAC variants are found in this region (PMID: 32628740, 30368667). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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Roifman syndrome Pathogenic:1
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Lowry-Wood syndrome;C1859452: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