rs9288516

Positions:

• chr2-216188541-T-A
• chr2-216188541-T-C
• chr2-216188541-T-G

Variant summary

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

The NM_021141.4(XRCC5):​c.1835-1684T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 152,290 control chromosomes in the GnomAD database, including 1,088 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 0.057 (1088 hom., cov: 32)
• Consequence: XRCC5 NM_021141.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

Genes affected

XRCC5 (HGNC:12833): (X-ray repair cross complementing 5) The protein encoded by this gene is the 80-kilodalton subunit of the Ku heterodimer protein which is also known as ATP-dependant DNA helicase II or DNA repair protein XRCC5. Ku is the DNA-binding component of the DNA-dependent protein kinase, and it functions together with the DNA ligase IV-XRCC4 complex in the repair of DNA double-strand break by non-homologous end joining and the completion of V(D)J recombination events. This gene functionally complements Chinese hamster xrs-6, a mutant defective in DNA double-strand break repair and in ability to undergo V(D)J recombination. A rare microsatellite polymorphism in this gene is associated with cancer in patients of varying radiosensitivity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XRCC5	NM_021141.4	c.1835-1684T>A		intron_variant		ENST00000392132.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XRCC5	ENST00000392132.7	c.1835-1684T>A		intron_variant		1	NM_021141.4	P1
XRCC5	ENST00000460284.5	n.2377-1684T>A		intron_variant, non_coding_transcript_variant		1
XRCC5	ENST00000392133.7	c.1835-1684T>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8708 AN: 152172 Hom.: 1082 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.0297

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0573 AC: 8719 AN: 152290 Hom.: 1088 Cov.: 32 AF XY: 0.0635 AC XY: 4727 AN XY: 74452

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.0478

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.0800

Gnomad4 FIN AF: 0.0297

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0346 Hom.: 53

Bravo AF: 0.0732

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.25
DANN	Benign	0.36

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: rs9288516; hg19: chr2-217053264;