rs886037606
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_StrongPP5
The NM_024782.3(NHEJ1):c.177+1_177+3delinsTT variant causes a splice donor, splice donor region, intron change. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 31)
Consequence
NHEJ1
NM_024782.3 splice_donor, splice_donor_region, intron
NM_024782.3 splice_donor, splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.44
Genes affected
NHEJ1 (HGNC:25737): (non-homologous end joining factor 1) Double-strand breaks in DNA result from genotoxic stresses and are among the most damaging of DNA lesions. This gene encodes a DNA repair factor essential for the nonhomologous end-joining pathway, which preferentially mediates repair of double-stranded breaks. Mutations in this gene cause different kinds of severe combined immunodeficiency disorders. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.19555555 fraction of the gene. Cryptic splice site detected, with MaxEntScore 4.2, offset of 0 (no position change), new splice context is: caaGTtagt. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PP5
?
Variant 2-219158183-TAC-AA is Pathogenic according to our data. Variant chr2-219158183-TAC-AA is described in ClinVar as [Pathogenic]. Clinvar id is 984.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHEJ1 | NM_024782.3 | c.177+1_177+3delinsTT | splice_donor_variant, splice_donor_region_variant, intron_variant | ENST00000356853.10 | |||
NHEJ1 | NM_001377498.1 | c.177+1_177+3delinsTT | splice_donor_variant, splice_donor_region_variant, intron_variant | ||||
NHEJ1 | NM_001377499.1 | c.177+1_177+3delinsTT | splice_donor_variant, splice_donor_region_variant, intron_variant | ||||
NHEJ1 | NR_165304.1 | n.273+1_273+3delinsTT | splice_donor_variant, splice_donor_region_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHEJ1 | ENST00000356853.10 | c.177+1_177+3delinsTT | splice_donor_variant, splice_donor_region_variant, intron_variant | 1 | NM_024782.3 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Cernunnos-XLF deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 27, 2006 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at