3-14145257-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004628.5(XPC):c.*684G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
XPC
NM_004628.5 3_prime_UTR
NM_004628.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0480
Publications
14 publications found
Genes affected
XPC (HGNC:12816): (XPC complex subunit, DNA damage recognition and repair factor) The protein encoded by this gene is a key component of the XPC complex, which plays an important role in the early steps of global genome nucleotide excision repair (NER). The encoded protein is important for damage sensing and DNA binding, and shows a preference for single-stranded DNA. Mutations in this gene or some other NER components can result in Xeroderma pigmentosum, a rare autosomal recessive disorder characterized by increased sensitivity to sunlight with the development of carcinomas at an early age. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152146Hom.: 0 Cov.: 33
GnomAD3 genomes
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152146
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33
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GnomAD2 exomes AF: 0.00000824 AC: 1AN: 121382 AF XY: 0.00 show subpopulations
GnomAD2 exomes
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1
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121382
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 534312Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 288628
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
534312
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
288628
African (AFR)
AF:
AC:
0
AN:
15372
American (AMR)
AF:
AC:
0
AN:
33752
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19136
East Asian (EAS)
AF:
AC:
0
AN:
32000
South Asian (SAS)
AF:
AC:
0
AN:
60242
European-Finnish (FIN)
AF:
AC:
0
AN:
32628
Middle Eastern (MID)
AF:
AC:
0
AN:
2376
European-Non Finnish (NFE)
AF:
AC:
0
AN:
308912
Other (OTH)
AF:
AC:
0
AN:
29894
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74316
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
152146
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74316
African (AFR)
AF:
AC:
0
AN:
41424
American (AMR)
AF:
AC:
0
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5198
South Asian (SAS)
AF:
AC:
0
AN:
4836
European-Finnish (FIN)
AF:
AC:
0
AN:
10586
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68038
Other (OTH)
AF:
AC:
0
AN:
2090
Alfa
AF:
Hom.:
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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