3-14145982-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004628.5(XPC):​c.2782A>C​(p.Lys928Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000478 in 1,608,788 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 28)
Exomes 𝑓: 0.00026 ( 2 hom. )

Consequence

XPC
NM_004628.5 missense

Scores

2
17

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5O:1

Conservation

PhyloP100: 1.52
Variant links:
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]
XPC-AS1 (HGNC:55014): (XPC antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0036734939).
BP6
Variant 3-14145982-T-G is Benign according to our data. Variant chr3-14145982-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 135472.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-14145982-T-G is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00261 (397/152108) while in subpopulation AFR AF= 0.00928 (385/41492). AF 95% confidence interval is 0.00851. There are 1 homozygotes in gnomad4. There are 178 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
XPCNM_004628.5 linkc.2782A>C p.Lys928Gln missense_variant Exon 16 of 16 ENST00000285021.12 NP_004619.3 Q01831-1X5DRB1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
XPCENST00000285021.12 linkc.2782A>C p.Lys928Gln missense_variant Exon 16 of 16 1 NM_004628.5 ENSP00000285021.8 Q01831-1
ENSG00000268279ENST00000608606.1 linkn.*198+299T>G intron_variant Intron 4 of 4 5 ENSP00000476275.1 V9GY05

Frequencies

GnomAD3 genomes
AF:
0.00261
AC:
396
AN:
151990
Hom.:
1
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.00928
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000524
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00192
GnomAD3 exomes
AF:
0.000563
AC:
140
AN:
248832
Hom.:
1
AF XY:
0.000430
AC XY:
58
AN XY:
135034
show subpopulations
Gnomad AFR exome
AF:
0.00794
Gnomad AMR exome
AF:
0.000378
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000558
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000266
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000255
AC:
372
AN:
1456680
Hom.:
2
Cov.:
37
AF XY:
0.000242
AC XY:
175
AN XY:
723636
show subpopulations
Gnomad4 AFR exome
AF:
0.00922
Gnomad4 AMR exome
AF:
0.000427
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000632
Gnomad4 OTH exome
AF:
0.000615
GnomAD4 genome
AF:
0.00261
AC:
397
AN:
152108
Hom.:
1
Cov.:
28
AF XY:
0.00239
AC XY:
178
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.00928
Gnomad4 AMR
AF:
0.000523
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00190
Alfa
AF:
0.000708
Hom.:
1
Bravo
AF:
0.00294
ESP6500AA
AF:
0.00601
AC:
23
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000629
AC:
76
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.00

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:5Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Xeroderma pigmentosum, group C Benign:2
Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -

Dec 05, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Xeroderma pigmentosum Benign:1
Nov 17, 2020
Sema4, Sema4
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: curation

- -

not provided Benign:1
Jan 20, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

XPC-related disorder Benign:1
Aug 14, 2024
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not specified Other:1
Sep 19, 2013
ITMI
Significance: not provided
Review Status: no classification provided
Collection Method: reference population

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.51
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
16
DANN
Benign
0.97
DEOGEN2
Benign
0.18
T
Eigen
Benign
-0.20
Eigen_PC
Benign
-0.37
FATHMM_MKL
Benign
0.28
N
LIST_S2
Benign
0.66
T
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.0037
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.3
M
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-1.6
N
REVEL
Benign
0.10
Sift
Benign
0.030
D
Sift4G
Uncertain
0.017
D
Polyphen
0.95
P
Vest4
0.17
MVP
0.19
MPC
0.23
ClinPred
0.037
T
GERP RS
2.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.16
gMVP
0.27

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: rs3731177; hg19: chr3-14187482; COSMIC: COSV99542833; COSMIC: COSV99542833; API