rs886060552
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_133433.4(NIPBL):c.-424T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NIPBL
NM_133433.4 5_prime_UTR
NM_133433.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.976
Publications
0 publications found
Genes affected
NIPBL (HGNC:28862): (NIPBL cohesin loading factor) This gene encodes the homolog of the Drosophila melanogaster Nipped-B gene product and fungal Scc2-type sister chromatid cohesion proteins. The Drosophila protein facilitates enhancer-promoter communication of remote enhancers and plays a role in developmental regulation. It is also homologous to a family of chromosomal adherins with broad roles in sister chromatid cohesion, chromosome condensation, and DNA repair. The human protein has a bipartite nuclear targeting sequence and a putative HEAT repeat. Condensins, cohesins and other complexes with chromosome-related functions also contain HEAT repeats. Mutations in this gene result in Cornelia de Lange syndrome, a disorder characterized by dysmorphic facial features, growth delay, limb reduction defects, and cognitive disability. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 61944Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
61944
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
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Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 18386Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 9536
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
18386
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
9536
African (AFR)
AF:
AC:
0
AN:
404
American (AMR)
AF:
AC:
0
AN:
504
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
484
East Asian (EAS)
AF:
AC:
0
AN:
1858
South Asian (SAS)
AF:
AC:
0
AN:
342
European-Finnish (FIN)
AF:
AC:
0
AN:
1714
Middle Eastern (MID)
AF:
AC:
0
AN:
88
European-Non Finnish (NFE)
AF:
AC:
0
AN:
11830
Other (OTH)
AF:
AC:
0
AN:
1162
GnomAD4 genome 0.00 AC: 0AN: 61944Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 29488
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
61944
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
29488
African (AFR)
AF:
AC:
0
AN:
16500
American (AMR)
AF:
AC:
0
AN:
6412
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1512
East Asian (EAS)
AF:
AC:
0
AN:
1370
South Asian (SAS)
AF:
AC:
0
AN:
1378
European-Finnish (FIN)
AF:
AC:
0
AN:
3860
Middle Eastern (MID)
AF:
AC:
0
AN:
122
European-Non Finnish (NFE)
AF:
AC:
0
AN:
29560
Other (OTH)
AF:
AC:
0
AN:
938
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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