5-36952018-CTGTGTG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_133433.4(NIPBL):c.-79-1569_-79-1564del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00047 ( 0 hom., cov: 0)
Consequence
NIPBL
NM_133433.4 intron
NM_133433.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.326
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 Benign. Variant got -10 ACMG points.
BP6
?
Variant 5-36952018-CTGTGTG-C is Benign according to our data. Variant chr5-36952018-CTGTGTG-C is described in ClinVar as [Likely_benign]. Clinvar id is 1879621.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000471 (48/101952) while in subpopulation EAS AF= 0.00387 (10/2586). AF 95% confidence interval is 0.0021. There are 0 homozygotes in gnomad4. There are 28 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High AC in GnomAd at 49 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIPBL | NM_133433.4 | c.-79-1569_-79-1564del | intron_variant | ENST00000282516.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIPBL | ENST00000282516.13 | c.-79-1569_-79-1564del | intron_variant | 1 | NM_133433.4 | P1 | |||
NIPBL | ENST00000448238.2 | c.-79-1569_-79-1564del | intron_variant | 1 | |||||
NIPBL | ENST00000652901.1 | c.-79-1569_-79-1564del | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000481 AC: 49AN: 101930Hom.: 0 Cov.: 0
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GnomAD4 genome ? AF: 0.000471 AC: 48AN: 101952Hom.: 0 Cov.: 0 AF XY: 0.000586 AC XY: 28AN XY: 47742
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | NIPBL: BS1 - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at