rs13312840

Positions:

• chr8-89985681-A-G
• chr8-89985681-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000396252.6(NBN):​c.-229-708T>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 151,326 control chromosomes in the GnomAD database, including 443 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.070 (443 hom., cov: 31)
• Consequence: NBN ENST00000396252.6 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NBN	ENST00000396252.6	c.-229-708T>C		intron_variant, NMD_transcript_variant		5		ENSP00000379551

Frequencies

GnomAD3 genomes AF: 0.0699 AC: 10569 AN: 151228 Hom.: 442 Cov.: 31

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0344

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0620

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0698 AC: 10563 AN: 151326 Hom.: 443 Cov.: 31 AF XY: 0.0708 AC XY: 5231 AN XY: 73890

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.0344

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0683 Hom.: 60

Bravo AF: 0.0658

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13312840; hg19: chr8-90997909;