GeneBe

rs778354452

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024782.3(NHEJ1):​c.826-116_826-103delAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000597 in 335,198 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 28)
Exomes 𝑓: 0.0000060 ( 0 hom. )

Consequence

NHEJ1
NM_024782.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.16

Publications

0 publications found
Variant links:
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]
NHEJ1 Gene-Disease associations (from GenCC):
  • Cernunnos-XLF deficiency
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024782.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NHEJ1
NM_024782.3
MANE Select
c.826-116_826-103delAAAAAAAAAAAAAA
intron
N/ANP_079058.1Q9H9Q4-1
NHEJ1
NM_001377499.1
c.841-116_841-103delAAAAAAAAAAAAAA
intron
N/ANP_001364428.1H7C0G7
NHEJ1
NM_001377498.1
c.826-116_826-103delAAAAAAAAAAAAAA
intron
N/ANP_001364427.1Q9H9Q4-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NHEJ1
ENST00000356853.10
TSL:1 MANE Select
c.826-116_826-103delAAAAAAAAAAAAAA
intron
N/AENSP00000349313.5Q9H9Q4-1
ENSG00000280537
ENST00000318673.6
TSL:2
n.*1948-116_*1948-103delAAAAAAAAAAAAAA
intron
N/AENSP00000320919.3F8W735
NHEJ1
ENST00000881108.1
c.892-116_892-103delAAAAAAAAAAAAAA
intron
N/AENSP00000551167.1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
AF:
0.00000597
AC:
2
AN:
335198
Hom.:
0
AF XY:
0.00000543
AC XY:
1
AN XY:
184004
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
8954
American (AMR)
AF:
0.00
AC:
0
AN:
15420
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9718
East Asian (EAS)
AF:
0.00
AC:
0
AN:
18096
South Asian (SAS)
AF:
0.0000231
AC:
1
AN:
43216
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
16880
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1290
European-Non Finnish (NFE)
AF:
0.00000490
AC:
1
AN:
204188
Other (OTH)
AF:
0.00
AC:
0
AN:
17436
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.700
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs778354452; hg19: chr2-219941279; API