chr3-14156046-A-G

Position:

• chr3-14156046-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004628.5(XPC):​c.2033+289T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 152,184 control chromosomes in the GnomAD database, including 171 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.040 (171 hom., cov: 32)
• Consequence: XPC NM_004628.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.33

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)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 3-14156046-A-G is Benign according to our data. Variant chr3-14156046-A-G is described in ClinVar as [Benign]. Clinvar id is 1273262.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.057 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XPC	NM_004628.5	c.2033+289T>C		intron_variant		ENST00000285021.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XPC	ENST00000285021.12	c.2033+289T>C		intron_variant		1	NM_004628.5	P1
XPC-AS1	ENST00000627116.2	n.456+6049A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6046 AN: 152066 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0397 AC: 6045 AN: 152184 Hom.: 171 Cov.: 32 AF XY: 0.0395 AC XY: 2942 AN XY: 74400

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0460

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0585

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0464 Hom.: 96

Bravo AF: 0.0384

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.026
DANN	Benign	0.56

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

Other links and lift over

dbSNP: rs3731143; hg19: chr3-14197546;