7-152648413-GAAAAAAA-GAAAAAAAA

Variant names:

• chr7-152648413-G-GA
• rs10707642
• NM_005431.2:c.*228dupT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_005431.2(XRCC2):​c.*228dupT 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 0.00052 (0 hom., cov: 0)
  • Exomes 𝑓: 0.018 (0 hom.)
• Consequence: XRCC2 NM_005431.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

Genes affected

XRCC2 (HGNC:12829): (X-ray repair cross complementing 2) This gene encodes a member of the RecA/Rad51-related protein family that participates in homologous recombination to maintain chromosome stability and repair DNA damage. This gene is involved in the repair of DNA double-strand breaks by homologous recombination and it functionally complements Chinese hamster irs1, a repair-deficient mutant that exhibits hypersensitivity to a number of different DNA-damaging agents. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000516 (73/141512) while in subpopulation AFR AF= 0.00098 (37/37762). AF 95% confidence interval is 0.00073. There are 0 homozygotes in gnomad4. There are 38 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XRCC2	NM_005431.2	c.*228dupT		3_prime_UTR_variant	Exon 3 of 3	ENST00000359321.2	NP_005422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XRCC2	ENST00000359321	c.*228dupT		3_prime_UTR_variant	Exon 3 of 3	1	NM_005431.2	ENSP00000352271.1
XRCC2	ENST00000495707.1	n.1093dupT		non_coding_transcript_exon_variant	Exon 3 of 3	1
XRCC2	ENST00000698506	c.*228dupT		3_prime_UTR_variant	Exon 2 of 2			ENSP00000513758.1

Frequencies

GnomAD3 genomes AF: 0.000509 AC: 72 AN: 141484 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000955

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000141

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000417

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000357

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000443

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0184 AC: 2177 AN: 118306 Hom.: 0 Cov.: 0 AF XY: 0.0187 AC XY: 1097 AN XY: 58816

Gnomad4 AFR exome AF: 0.0223

Gnomad4 AMR exome AF: 0.0208

Gnomad4 ASJ exome AF: 0.0295

Gnomad4 EAS exome AF: 0.0103

Gnomad4 SAS exome AF: 0.0146

Gnomad4 FIN exome AF: 0.0138

Gnomad4 NFE exome AF: 0.0185

Gnomad4 OTH exome AF: 0.0216

GnomAD4 genome AF: 0.000516 AC: 73 AN: 141512 Hom.: 0 Cov.: 0 AF XY: 0.000555 AC XY: 38 AN XY: 68408

Gnomad4 AFR AF: 0.000980

Gnomad4 AMR AF: 0.000141

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000418

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000357

Gnomad4 NFE AF: 0.000443

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs10707642; hg19: chr7-152345498;