chr19-43543341-C-CGTGTGTGTGTGTGT

Variant names:

• chr19-43543341-C-CGTGTGTGTGTGTGT
• rs45592142
• ENST00000262887:c.*37_*50dupACACACACACACAC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_006297.3(XRCC1):​c.*37_*50dupACACACACACACAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0017 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00032 (0 hom.)
• Consequence: XRCC1 NM_006297.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XRCC1	NM_006297.3	c.*37_*50dupACACACACACACAC		3_prime_UTR_variant	Exon 17 of 17	ENST00000262887.10	NP_006288.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XRCC1	ENST00000262887	c.*37_*50dupACACACACACACAC		3_prime_UTR_variant	Exon 17 of 17	1	NM_006297.3	ENSP00000262887.5
XRCC1	ENST00000543982	c.*37_*50dupACACACACACACAC		3_prime_UTR_variant	Exon 16 of 16	2		ENSP00000443671.1

Frequencies

GnomAD3 genomes AF: 0.00169 AC: 235 AN: 139218 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00329

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00407

Gnomad ASJ AF: 0.00118

Gnomad EAS AF: 0.000212

Gnomad SAS AF: 0.000232

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00993

Gnomad NFE AF: 0.000703

Gnomad OTH AF: 0.00370

GnomAD4 exome AF: 0.000319 AC: 289 AN: 905104 Hom.: 0 Cov.: 0 AF XY: 0.000316 AC XY: 147 AN XY: 465720

Gnomad4 AFR exome AF: 0.00254

Gnomad4 AMR exome AF: 0.000718

Gnomad4 ASJ exome AF: 0.00137

Gnomad4 EAS exome AF: 0.0000278

Gnomad4 SAS exome AF: 0.000383

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000203

Gnomad4 OTH exome AF: 0.000484

GnomAD4 genome AF: 0.00169 AC: 235 AN: 139320 Hom.: 1 Cov.: 0 AF XY: 0.00165 AC XY: 111 AN XY: 67318

Gnomad4 AFR AF: 0.00328

Gnomad4 AMR AF: 0.00407

Gnomad4 ASJ AF: 0.00118

Gnomad4 EAS AF: 0.000212

Gnomad4 SAS AF: 0.000232

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000703

Gnomad4 OTH AF: 0.00366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs45592142; hg19: chr19-44047493;