Variant rs3218425 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005431.2(XRCC2):c.40-6836_40-6832del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 151,256 control chromosomes in the GnomAD database, including 2,426 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2426 hom., cov: 26)

Consequence

XRCC2
NM_005431.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Variant links:

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]

XRCC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XRCC2	NM_005431.2 linkuse as main transcript	c.40-6836_40-6832del		intron_variant		ENST00000359321.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
XRCC2	ENST00000359321.2 linkuse as main transcript	c.40-6836_40-6832del	intron_variant	1	NM_005431.2	P1
XRCC2	ENST00000698506.1 linkuse as main transcript	c.-48+8423_-48+8427del	intron_variant
XRCC2	ENST00000698507.1 linkuse as main transcript	n.108-6836_108-6832del	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25127

AN:

151142

Hom.:

2425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0634

Gnomad AMI

AF:

0.0496

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.151

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

GnomAD4 genome

AF:

0.166

AC:

25119

AN:

151256

Hom.:

2426

Cov.:

AF XY:

0.165

AC XY:

12191

AN XY:

73864

show subpopulations

Gnomad4 AFR

AF:

0.0633

Gnomad4 AMR

AF:

0.143

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.226

Gnomad4 FIN

AF:

0.222

Gnomad4 NFE

AF:

0.225

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.192

Hom.:

360

Bravo

AF:

0.155

Asia WGS

AF:

0.171

AC:

593

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over