7-152676167-C-G

Position:

• chr7-152676167-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000698506.1(XRCC2):​c.-174G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,588,906 control chromosomes in the GnomAD database, including 37,420 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.17 (2583 hom., cov: 34)
  • Exomes 𝑓: 0.22 (34837 hom.)
• Consequence: XRCC2 ENST00000698506.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.942

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 7-152676167-C-G is Benign according to our data. Variant chr7-152676167-C-G is described in ClinVar as [Benign]. Clinvar id is 1265138.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.152676167C>G		intergenic_region
XRCC2	NM_005431.2	c.-88G>C		upstream_gene_variant		ENST00000359321.2	NP_005422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XRCC2	ENST00000698506.1	c.-174G>C		5_prime_UTR_variant	1/2			ENSP00000513758.1
XRCC2	ENST00000359321.2	c.-88G>C		upstream_gene_variant		1	NM_005431.2	ENSP00000352271.1
XRCC2	ENST00000698507.1	n.-20G>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26273 AN: 152182 Hom.: 2581 Cov.: 34

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.158

GnomAD4 exome AF: 0.216 AC: 310326 AN: 1436604 Hom.: 34837 Cov.: 26 AF XY: 0.217 AC XY: 155513 AN XY: 715512

Gnomad4 AFR exome AF: 0.0782

Gnomad4 AMR exome AF: 0.102

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.135

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.224

Gnomad4 NFE exome AF: 0.228

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.173 AC: 26280 AN: 152302 Hom.: 2583 Cov.: 34 AF XY: 0.172 AC XY: 12806 AN XY: 74464

Gnomad4 AFR AF: 0.0830

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.158

Alfa AF: 0.113 Hom.: 187

Bravo AF: 0.162

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3218384; hg19: chr7-152373252; COSMIC: COSV63771224;