5-37064967-CAAA-CAA
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_133433.4(NIPBL):c.*84del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.000337 in 1,526,394 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00037 ( 0 hom. )
Consequence
NIPBL
NM_133433.4 3_prime_UTR
NM_133433.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.35
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 made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 5-37064967-CA-C is Benign according to our data. Variant chr5-37064967-CA-C is described in ClinVar as [Benign]. Clinvar id is 159023.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 512 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIPBL | NM_133433.4 | c.*84del | 3_prime_UTR_variant | 47/47 | ENST00000282516.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIPBL | ENST00000282516.13 | c.*84del | 3_prime_UTR_variant | 47/47 | 1 | NM_133433.4 | P1 | ||
NIPBL | ENST00000652901.1 | c.*443del | 3_prime_UTR_variant | 46/46 | |||||
NIPBL | ENST00000514335.1 | n.2422del | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000201 AC: 3AN: 149282Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000372 AC: 512AN: 1377000Hom.: 0 Cov.: 23 AF XY: 0.000387 AC XY: 266AN XY: 687394
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GnomAD4 genome AF: 0.0000201 AC: 3AN: 149394Hom.: 0 Cov.: 32 AF XY: 0.0000137 AC XY: 1AN XY: 72772
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at