chr19-43545709-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006297.3(XRCC1):c.1621+109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
XRCC1
NM_006297.3 intron
NM_006297.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00100
Publications
8 publications found
Genes affected
XRCC1 (HGNC:12828): (X-ray repair cross complementing 1) The protein encoded by this gene is involved in the efficient repair of DNA single-strand breaks formed by exposure to ionizing radiation and alkylating agents. This protein interacts with DNA ligase III, polymerase beta and poly (ADP-ribose) polymerase to participate in the base excision repair pathway. It may play a role in DNA processing during meiogenesis and recombination in germ cells. A rare microsatellite polymorphism in this gene is associated with cancer in patients of varying radiosensitivity. [provided by RefSeq, Jul 2008]
XRCC1 Gene-Disease associations (from GenCC):
- head and neck cancerInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- spinocerebellar ataxia, autosomal recessive 26Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1283358Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 635568
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1283358
Hom.:
AF XY:
AC XY:
0
AN XY:
635568
African (AFR)
AF:
AC:
0
AN:
29254
American (AMR)
AF:
AC:
0
AN:
34022
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20166
East Asian (EAS)
AF:
AC:
0
AN:
38500
South Asian (SAS)
AF:
AC:
0
AN:
71214
European-Finnish (FIN)
AF:
AC:
0
AN:
46404
Middle Eastern (MID)
AF:
AC:
0
AN:
5178
European-Non Finnish (NFE)
AF:
AC:
0
AN:
984846
Other (OTH)
AF:
AC:
0
AN:
53774
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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