chr4-26386337-AT-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_015874.6(RBPJ):c.21-5del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.57 ( 24380 hom., cov: 0)
Exomes 𝑓: 0.58 ( 180522 hom. )
Consequence
RBPJ
NM_015874.6 splice_polypyrimidine_tract, intron
NM_015874.6 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.300
Genes affected
RBPJ (HGNC:5724): (recombination signal binding protein for immunoglobulin kappa J region) The protein encoded by this gene is a transcriptional regulator important in the Notch signaling pathway. The encoded protein acts as a repressor when not bound to Notch proteins and an activator when bound to Notch proteins. It is thought to function by recruiting chromatin remodeling complexes containing histone deacetylase or histone acetylase proteins to Notch signaling pathway genes. Several transcript variants encoding different isoforms have been found for this gene, and several pseudogenes of this gene exist on chromosome 9. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 4-26386337-AT-A is Benign according to our data. Variant chr4-26386337-AT-A is described in ClinVar as [Benign]. Clinvar id is 1164945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBPJ | NM_015874.6 | c.21-5del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000355476.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBPJ | ENST00000355476.8 | c.21-5del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015874.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.572 AC: 85587AN: 149536Hom.: 24341 Cov.: 0
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GnomAD3 exomes AF: 0.628 AC: 119655AN: 190628Hom.: 31063 AF XY: 0.627 AC XY: 64295AN XY: 102516
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GnomAD4 exome AF: 0.580 AC: 724816AN: 1249684Hom.: 180522 Cov.: 0 AF XY: 0.581 AC XY: 361813AN XY: 622508
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GnomAD4 genome ? AF: 0.573 AC: 85680AN: 149646Hom.: 24380 Cov.: 0 AF XY: 0.574 AC XY: 41906AN XY: 73014
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 27, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at