rs6884762

chr5-132603038-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_005732.4(RAD50):c.2208-262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 152,276 control chromosomes in the GnomAD database, including 39 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 0.018 (39 hom., cov: 32)
• Consequence: RAD50 NM_005732.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

Genes affected

RAD50 (HGNC:9816): (RAD50 double strand break repair protein) The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Rad50, a protein involved in DNA double-strand break repair. This protein forms a complex with MRE11 and NBS1. The protein complex binds to DNA and displays numerous enzymatic activities that are required for nonhomologous joining of DNA ends. This protein, cooperating with its partners, is important for DNA double-strand break repair, cell cycle checkpoint activation, telomere maintenance, and meiotic recombination. Knockout studies of the mouse homolog suggest this gene is essential for cell growth and viability. Mutations in this gene are the cause of Nijmegen breakage syndrome-like disorder.[provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0184 (2797/152276) while in subpopulation NFE AF= 0.0283 (1927/68022). AF 95% confidence interval is 0.0273. There are 39 homozygotes in gnomad4. There are 1332 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 39 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD50	NM_005732.4	c.2208-262C>T		intron_variant		ENST00000378823.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD50	ENST00000378823.8	c.2208-262C>T		intron_variant		1	NM_005732.4	P1

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2798 AN: 152158 Hom.: 39 Cov.: 32

Gnomad AFR AF: 0.00422

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.00936

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0192

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

GnomAD4 genome AF: 0.0184 AC: 2797 AN: 152276 Hom.: 39 Cov.: 32 AF XY: 0.0179 AC XY: 1332 AN XY: 74452

Gnomad4 AFR AF: 0.00421

Gnomad4 AMR AF: 0.00935

Gnomad4 ASJ AF: 0.0479

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0155

Gnomad4 FIN AF: 0.0234

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.0190

Alfa AF: 0.0264 Hom.: 33

Bravo AF: 0.0166

Asia WGS AF: 0.00549 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.0
Dann	Benign	0.25

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

Other links and lift over

dbSNP: rs6884762; hg19: chr5-131938730;