chr20-45309178-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_014276.4(RBPJL):c.132-389T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 151,866 control chromosomes in the GnomAD database, including 448 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.051 ( 448 hom., cov: 31)
Consequence
RBPJL
NM_014276.4 intron
NM_014276.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0640
Genes affected
RBPJL (HGNC:13761): (recombination signal binding protein for immunoglobulin kappa J region like) This gene encodes a member of the suppressor of hairless protein family. A similar protein in mouse is a transcription factor that binds to DNA sequences almost identical to that bound by the Notch receptor signaling pathway transcription factor recombining binding protein J. The mouse protein has been shown to activate transcription in concert with Epstein-Barr virus nuclear antigen-2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 20-45309178-T-C is Benign according to our data. Variant chr20-45309178-T-C is described in ClinVar as [Benign]. Clinvar id is 444114.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBPJL | NM_014276.4 | c.132-389T>C | intron_variant | ENST00000343694.8 | |||
RBPJL | NM_001281448.2 | c.132-389T>C | intron_variant | ||||
RBPJL | NM_001281449.2 | c.132-389T>C | intron_variant | ||||
RBPJL | XM_011528522.3 | c.132-389T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBPJL | ENST00000343694.8 | c.132-389T>C | intron_variant | 1 | NM_014276.4 | A1 | |||
RBPJL | ENST00000372741.7 | c.132-389T>C | intron_variant | 1 | |||||
RBPJL | ENST00000372743.5 | c.132-389T>C | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0509 AC: 7731AN: 151752Hom.: 447 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0509 AC: 7724AN: 151866Hom.: 448 Cov.: 31 AF XY: 0.0520 AC XY: 3863AN XY: 74238
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684
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Type 2 diabetes mellitus Benign:1
Benign, no assertion criteria provided | case-control | Diabetes Molecular Genetics Section, Phoenix Epidemiology and Clinical Research Branch, National Institutes of Health | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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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