rs2734823

Variant names:

• chr8-89931500-A-G
• rs2734823
• ENST00000697293:c.*4082T>C

Variant summary

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

The ENST00000517337(NBN):​c.*4082T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,972 control chromosomes in the GnomAD database, including 24,146 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 0.53 (24146 hom., cov: 32)
• Consequence: NBN ENST00000517337 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NBN	ENST00000697293	c.*4082T>C		3_prime_UTR_variant	Exon 17 of 17			ENSP00000513230.1
NBN	ENST00000517337	c.*4082T>C		3_prime_UTR_variant	Exon 17 of 17	4		ENSP00000429971.2
NBN	ENST00000697298	c.*4082T>C		3_prime_UTR_variant	Exon 18 of 18			ENSP00000513234.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80319 AN: 151854 Hom.: 24074 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.529 AC: 80467 AN: 151972 Hom.: 24146 Cov.: 32 AF XY: 0.528 AC XY: 39203 AN XY: 74268

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.504

Alfa AF: 0.470 Hom.: 2443

Bravo AF: 0.550

Asia WGS AF: 0.615 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734823; hg19: chr8-90943728;