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GeneBe

rs3835

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_021141.4(XRCC5):c.2110-2408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,168 control chromosomes in the GnomAD database, including 4,611 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 4611 hom., cov: 32)

Consequence

XRCC5
NM_021141.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.42
Variant links:
Genes affected
XRCC5 (HGNC:12833): (X-ray repair cross complementing 5) The protein encoded by this gene is the 80-kilodalton subunit of the Ku heterodimer protein which is also known as ATP-dependant DNA helicase II or DNA repair protein XRCC5. Ku is the DNA-binding component of the DNA-dependent protein kinase, and it functions together with the DNA ligase IV-XRCC4 complex in the repair of DNA double-strand break by non-homologous end joining and the completion of V(D)J recombination events. This gene functionally complements Chinese hamster xrs-6, a mutant defective in DNA double-strand break repair and in ability to undergo V(D)J recombination. A rare microsatellite polymorphism in this gene is associated with cancer in patients of varying radiosensitivity. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
XRCC5NM_021141.4 linkuse as main transcriptc.2110-2408G>A intron_variant ENST00000392132.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
XRCC5ENST00000392132.7 linkuse as main transcriptc.2110-2408G>A intron_variant 1 NM_021141.4 P1
XRCC5ENST00000460284.5 linkuse as main transcriptn.2652-2408G>A intron_variant, non_coding_transcript_variant 1
XRCC5ENST00000392133.7 linkuse as main transcriptc.2110-2408G>A intron_variant 5 P1

Frequencies

GnomAD3 genomes
AF:
0.205
AC:
31148
AN:
152050
Hom.:
4587
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.424
Gnomad AMI
AF:
0.0680
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.137
Gnomad EAS
AF:
0.0718
Gnomad SAS
AF:
0.172
Gnomad FIN
AF:
0.113
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.122
Gnomad OTH
AF:
0.163
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.205
AC:
31231
AN:
152168
Hom.:
4611
Cov.:
32
AF XY:
0.204
AC XY:
15192
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.424
Gnomad4 AMR
AF:
0.132
Gnomad4 ASJ
AF:
0.137
Gnomad4 EAS
AF:
0.0722
Gnomad4 SAS
AF:
0.173
Gnomad4 FIN
AF:
0.113
Gnomad4 NFE
AF:
0.122
Gnomad4 OTH
AF:
0.161
Alfa
AF:
0.152
Hom.:
681
Bravo
AF:
0.215
Asia WGS
AF:
0.149
AC:
519
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.29
Cadd
Benign
19
Dann
Benign
0.74

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

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

Other links and lift over

dbSNP: rs3835; hg19: chr2-217066637; API