2-121530887-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP5BP4BS2_Supporting

The NM_001395891.1(CLASP1):​c.196-562G>A variant causes a intron change. The variant allele was found at a frequency of 0.000426 in 692,974 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

Genomes: 𝑓 0.00039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00043 ( 0 hom. )

Consequence

CLASP1
NM_001395891.1 intron

Scores

2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5U:2

Conservation

PhyloP100: 5.74
Variant links:
Genes affected
CLASP1 (HGNC:17088): (cytoplasmic linker associated protein 1) CLASPs, such as CLASP1, are nonmotor microtubule-associated proteins that interact with CLIPs (e.g., CLIP170; MIM 179838). CLASP1 is involved in the regulation of microtubule dynamics at the kinetochore and throughout the spindle (Maiato et al., 2003 [PubMed 12837247]).[supplied by OMIM, Mar 2008]
RNU4ATAC (HGNC:34016): (RNA, U4atac small nuclear) The small nuclear RNA (snRNA) encoded by this gene is part of the U12-dependent minor spliceosome complex. In addition to the encoded RNA, this ribonucleoprotein complex consists of U11, U12, U5, and U6atac snRNAs. The U12-dependent spliceosome acts on approximately 700 specific introns in the human genome. Defects in this gene are a cause of microcephalic osteodysplastic primordial dwarfism type 1 (MOPD). [provided by RefSeq, Jul 2011]
CLASP1-AS1 (HGNC:55328): (CLASP1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PP5
Variant 2-121530887-C-T is Pathogenic according to our data. Variant chr2-121530887-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 218086.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Pathogenic=1, Likely_pathogenic=3}. Variant chr2-121530887-C-T is described in Lovd as [Pathogenic]. Variant chr2-121530887-C-T is described in Lovd as [Likely_pathogenic].
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.22). . Strength limited to SUPPORTING due to the PP5.
BS2
High AC in GnomAd4 at 60 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CLASP1NM_001395891.1 linkc.196-562G>A intron_variant ENST00000696935.1 NP_001382820.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CLASP1ENST00000696935.1 linkc.196-562G>A intron_variant NM_001395891.1 ENSP00000512981.1 A0A8V8TLP7

Frequencies

GnomAD3 genomes
AF:
0.000394
AC:
60
AN:
152174
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000770
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000588
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000386
AC:
50
AN:
129556
Hom.:
0
AF XY:
0.000410
AC XY:
29
AN XY:
70760
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000332
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000385
Gnomad SAS exome
AF:
0.000539
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000486
Gnomad OTH exome
AF:
0.000504
GnomAD4 exome
AF:
0.000435
AC:
235
AN:
540682
Hom.:
0
Cov.:
0
AF XY:
0.000453
AC XY:
132
AN XY:
291570
show subpopulations
Gnomad4 AFR exome
AF:
0.000128
Gnomad4 AMR exome
AF:
0.000465
Gnomad4 ASJ exome
AF:
0.0000502
Gnomad4 EAS exome
AF:
0.000314
Gnomad4 SAS exome
AF:
0.000529
Gnomad4 FIN exome
AF:
0.0000906
Gnomad4 NFE exome
AF:
0.000527
Gnomad4 OTH exome
AF:
0.000167
GnomAD4 genome
AF:
0.000394
AC:
60
AN:
152292
Hom.:
0
Cov.:
32
AF XY:
0.000336
AC XY:
25
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.000241
Gnomad4 AMR
AF:
0.000261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000772
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000588
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000171
Hom.:
0
Bravo
AF:
0.000408
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:5Uncertain:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Pathogenic:2
Likely pathogenic, criteria provided, single submitterclinical testingBlueprint GeneticsNov 30, 2019- -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024This 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 (rs370715569, gnomAD 0.05%). This variant has been observed in individual(s) with clinical features of RNU4ATAC-related conditions (PMID: 26522830; Invitae). 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: 218086). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Functional studies have shown that this variant disrupts ncRNA function (PMID: 32628740). For these reasons, this variant has been classified as Pathogenic. -
Roifman syndrome Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMNov 02, 2015- -
RNU4ATAC-related disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJan 18, 2023The RNU4ATAC n.8C>T is a noncoding alteration. This variant has been reported in the compound heterozygous state in an individual with Roifman syndrome (Subject 6, Kindred K4, Merico et al. 2015. PubMed ID: 26522830). This variant is located in an element of major importance for splicing and is classified as a Roifman syndrome causal variant (Figure 3, Merico et al. 2015. PubMed ID: 26522830). A different substitution affecting the same nucleotide (n.8C>A) has been reported in the compound heterozygous state in an individual with Lowry-Wood syndrome (Shelihan et al. 2018. PubMed ID: 30368667). This variant is reported in 0.054% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-122288463-C-T). This variant is interpreted as likely pathogenic. -
Spondyloepiphyseal dysplasia congenita Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsMar 04, 2020- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJun 01, 2022Variant summary: RNU4ATAC n.8C>T alters a nucleotide in the non-coding RNA and located in Stem II region (n.3-n.19, element of major importance for splicing; Merico_2015) of RNU4ATAC. Additionally, Stem II, which base pair the U6atac, required to form the catalytically active minor spliceosome (PMID: 29263834). The variant allele was found at a frequency of 0.00039 in 129556 control chromosomes (gnomAD). n.8C>T has been reported in the literature in at least one compound heterozygous individual affected with Roifman Syndrome (Merico_2015) and one individual with RNU4ATAC-related conditions reported in one ClinVar lab. These data indicate that the variant may be associated with disease. At least one functional study reports this variant results in reducing splicing efficiency in transfected cells (Benoit-Pilven_2020). Five ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=1), likely pathogenic (n=3) and pathogenic (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Craniosynostosis syndrome;C0349588:Short stature;C0878544:Cardiomyopathy;C4022738:Neurodevelopmental delay;C4551563:Microcephaly Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLaboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert EinsteinApr 20, 2021ACMG classification criteria: PS3 supporting, PM3 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.22
CADD
Benign
20
DANN
Benign
0.96

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs370715569; hg19: chr2-122288463; API