rs13312970

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000265433.8(NBN):​c.2234+88C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 1,063,834 control chromosomes in the GnomAD database, including 1,621 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 433 hom., cov: 32)
Exomes 𝑓: 0.042 ( 1188 hom. )

Consequence

NBN
ENST00000265433.8 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.771
Variant links:
Genes affected
NBN (HGNC:7652): (nibrin) Mutations in this gene are associated with Nijmegen breakage syndrome, an autosomal recessive chromosomal instability syndrome characterized by microcephaly, growth retardation, immunodeficiency, and cancer predisposition. The encoded protein is a member of the MRE11/RAD50 double-strand break repair complex which consists of 5 proteins. This gene product is thought to be involved in DNA double-strand break repair and DNA damage-induced checkpoint activation. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 8-89936938-G-C is Benign according to our data. Variant chr8-89936938-G-C is described in ClinVar as [Benign]. Clinvar id is 1232508.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NBNNM_002485.5 linkuse as main transcriptc.2234+88C>G intron_variant ENST00000265433.8 NP_002476.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NBNENST00000265433.8 linkuse as main transcriptc.2234+88C>G intron_variant 1 NM_002485.5 ENSP00000265433 P1

Frequencies

GnomAD3 genomes
AF:
0.0600
AC:
9124
AN:
152070
Hom.:
427
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.122
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.0577
Gnomad ASJ
AF:
0.0398
Gnomad EAS
AF:
0.0553
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.00933
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0299
Gnomad OTH
AF:
0.0602
GnomAD4 exome
AF:
0.0415
AC:
37847
AN:
911646
Hom.:
1188
AF XY:
0.0432
AC XY:
20465
AN XY:
473746
show subpopulations
Gnomad4 AFR exome
AF:
0.122
Gnomad4 AMR exome
AF:
0.0492
Gnomad4 ASJ exome
AF:
0.0433
Gnomad4 EAS exome
AF:
0.0689
Gnomad4 SAS exome
AF:
0.0938
Gnomad4 FIN exome
AF:
0.00825
Gnomad4 NFE exome
AF:
0.0323
Gnomad4 OTH exome
AF:
0.0457
GnomAD4 genome
AF:
0.0601
AC:
9147
AN:
152188
Hom.:
433
Cov.:
32
AF XY:
0.0593
AC XY:
4416
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.122
Gnomad4 AMR
AF:
0.0577
Gnomad4 ASJ
AF:
0.0398
Gnomad4 EAS
AF:
0.0556
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.00933
Gnomad4 NFE
AF:
0.0298
Gnomad4 OTH
AF:
0.0667
Alfa
AF:
0.0455
Hom.:
38
Bravo
AF:
0.0652
Asia WGS
AF:
0.109
AC:
383
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -
Hereditary breast ovarian cancer syndrome Benign:1
Benign, criteria provided, single submitterclinical testingNational Health Laboratory Service, Universitas Academic Hospital and University of the Free StateApr 19, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.9
DANN
Benign
0.44

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13312970; hg19: chr8-90949166; COSMIC: COSV104545375; API