7-152648413-GAA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005431.2(XRCC2):c.*227_*228del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 259,274 control chromosomes in the GnomAD database, including 2,782 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2376 hom., cov: 0)
  • Exomes 𝑓: 0.23 (406 hom.)
• Consequence: XRCC2 NM_005431.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.347

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 -10 ACMG points.

• BP6: Variant 7-152648413-GAA-G is Benign according to our data. Variant chr7-152648413-GAA-G is described in ClinVar as [Benign]. Clinvar id is 1291098.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XRCC2	NM_005431.2	c.*227_*228del		3_prime_UTR_variant	3/3	ENST00000359321.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XRCC2	ENST00000359321.2	c.*227_*228del		3_prime_UTR_variant	3/3	1	NM_005431.2	P1
XRCC2	ENST00000495707.1	n.1092_1093del		non_coding_transcript_exon_variant	3/3	1
XRCC2	ENST00000698506.1	c.*227_*228del		3_prime_UTR_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.173 AC: 24520 AN: 141400 Hom.: 2376 Cov.: 0

Gnomad AFR AF: 0.0679

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.158

GnomAD4 exome AF: 0.233 AC: 27481 AN: 117846 Hom.: 406 AF XY: 0.234 AC XY: 13706 AN XY: 58602

Gnomad4 AFR exome AF: 0.132

Gnomad4 AMR exome AF: 0.175

Gnomad4 ASJ exome AF: 0.179

Gnomad4 EAS exome AF: 0.191

Gnomad4 SAS exome AF: 0.267

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.248

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.173 AC: 24508 AN: 141428 Hom.: 2376 Cov.: 0 AF XY: 0.173 AC XY: 11794 AN XY: 68354

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.158

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 07, 2019

- -

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: rs10707642; hg19: chr7-152345498;