Genetic Variant NHEJ1:c.826-119_826-103dupAAAAAAAAAAAAAAAAA (chr2-219076557-C-CTTTTTTTTTTTTTTTTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_024782.3(NHEJ1):c.826-119_826-103dupAAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_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: 𝑓 0.0 ( 0 hom., cov: 28)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NHEJ1
NM_024782.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.188

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

NHEJ1 links:

ENSG00000280537 (HGNC:):

ENSG00000280537 links:

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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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NHEJ1	NM_024782.3	MANE Select	c.826-119_826-103dupAAAAAAAAAAAAAAAAA	intron	N/A	NP_079058.1	Q9H9Q4-1
NHEJ1	NM_001377499.1		c.841-119_841-103dupAAAAAAAAAAAAAAAAA	intron	N/A	NP_001364428.1	H7C0G7
NHEJ1	NM_001377498.1		c.826-119_826-103dupAAAAAAAAAAAAAAAAA	intron	N/A	NP_001364427.1	Q9H9Q4-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NHEJ1	ENST00000356853.10	TSL:1 MANE Select	c.826-103_826-102insAAAAAAAAAAAAAAAAA	intron	N/A	ENSP00000349313.5	Q9H9Q4-1
ENSG00000280537	ENST00000318673.6	TSL:2	n.1948-103_1948-102insAAAAAAAAAAAAAAAAA	intron	N/A	ENSP00000320919.3	F8W735
NHEJ1	ENST00000881108.1		c.892-103_892-102insAAAAAAAAAAAAAAAAA	intron	N/A	ENSP00000551167.1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

122536

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

335198

Hom.:

AF XY:

0.00

AC XY:

AN XY:

184004

African (AFR)

AF:

0.00

AC:

AN:

8954

American (AMR)

AF:

0.00

AC:

AN:

15420

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9718

East Asian (EAS)

AF:

0.00

AC:

AN:

18096

South Asian (SAS)

AF:

0.00

AC:

AN:

43216

European-Finnish (FIN)

AF:

0.00

AC:

AN:

16880

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1290

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

204188

Other (OTH)

AF:

0.00

AC:

AN:

17436

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

122536

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

58630

African (AFR)

AF:

0.00

AC:

AN:

32606

American (AMR)

AF:

0.00

AC:

AN:

11814

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2976

East Asian (EAS)

AF:

0.00

AC:

AN:

4418

South Asian (SAS)

AF:

0.00

AC:

AN:

3900

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6128

Middle Eastern (MID)

AF:

0.00

AC:

AN:

252

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

57998

Other (OTH)

AF:

0.00

AC:

AN:

1654

Alfa

AF:

0.000231

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.19

Splicing

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

Publications

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2-219076557-CTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over