rs16384

Positions:

• chr22-41649005-A-AAAC
• chr22-41649005-A-AAAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001469.5(XRCC6):​c.961-1717_961-1716insACA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (53893 hom., cov: 0)
• Consequence: XRCC6 NM_001469.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

XRCC6 (HGNC:4055): (X-ray repair cross complementing 6) The p70/p80 autoantigen is a nuclear complex consisting of two subunits with molecular masses of approximately 70 and 80 kDa. The complex functions as a single-stranded DNA-dependent ATP-dependent helicase. The complex may be involved in the repair of nonhomologous DNA ends such as that required for double-strand break repair, transposition, and V(D)J recombination. High levels of autoantibodies to p70 and p80 have been found in some patients with systemic lupus erythematosus. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XRCC6	NM_001469.5	c.961-1717_961-1716insACA		intron_variant		ENST00000360079.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XRCC6	ENST00000360079.8	c.961-1717_961-1716insACA		intron_variant		1	NM_001469.5	P1

Frequencies

GnomAD3 genomes AF: 0.838 AC: 126366 AN: 150788 Hom.: 53844 Cov.: 0

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.838 AC: 126465 AN: 150898 Hom.: 53893 Cov.: 0 AF XY: 0.830 AC XY: 61124 AN XY: 73612

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.807

Alfa AF: 0.784 Hom.: 2001

Bravo AF: 0.827

Asia WGS AF: 0.838 AC: 2911 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16384; hg19: chr22-42045009;