rs3218417

Positions:

• chr7-152668549-AC-A

Variant summary

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

The NM_005431.2(XRCC2):​c.39+7491del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,058 control chromosomes in the GnomAD database, including 5,206 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5206 hom., cov: 21)
• Consequence: XRCC2 NM_005431.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

XRCC2 (HGNC:12829): (X-ray repair cross complementing 2) This gene encodes a member of the RecA/Rad51-related protein family that participates in homologous recombination to maintain chromosome stability and repair DNA damage. This gene is involved in the repair of DNA double-strand breaks by homologous recombination and it functionally complements Chinese hamster irs1, a repair-deficient mutant that exhibits hypersensitivity to a number of different DNA-damaging agents. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XRCC2	NM_005431.2	c.39+7491del		intron_variant		ENST00000359321.2	NP_005422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XRCC2	ENST00000359321.2	c.39+7491del		intron_variant		1	NM_005431.2	ENSP00000352271	P1
XRCC2	ENST00000698506.1	c.-48+7491del		intron_variant				ENSP00000513758
XRCC2	ENST00000698507.1	n.107+7491del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39389 AN: 151940 Hom.: 5200 Cov.: 21

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0694

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.259 AC: 39415 AN: 152058 Hom.: 5206 Cov.: 21 AF XY: 0.258 AC XY: 19196 AN XY: 74314

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.234

Alfa AF: 0.254 Hom.: 594

Bravo AF: 0.255

Asia WGS AF: 0.272 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3218417; hg19: chr7-152365634;