10-93208991-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000420392.1(XRCC6P1):n.352G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 1,378,160 control chromosomes in the GnomAD database, including 1,208 homozygotes. 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 0.037 (177 hom., cov: 32)
  • Exomes 𝑓: 0.033 (1031 hom.)
• Consequence: XRCC6P1 ENST00000420392.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

XRCC6P1 (HGNC:45183): (X-ray repair cross complementing 6 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0368 (5605/152254) while in subpopulation NFE AF= 0.0462 (3141/68022). AF 95% confidence interval is 0.0448. There are 177 homozygotes in gnomad4. There are 2987 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 177 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XRCC6P1	ENST00000420392.1	n.352G>A		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes AF: 0.0369 AC: 5607 AN: 152136 Hom.: 177 Cov.: 32

Gnomad AFR AF: 0.00874

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0312

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0359

GnomAD4 exome AF: 0.0333 AC: 40838 AN: 1225906 Hom.: 1031 Cov.: 26 AF XY: 0.0336 AC XY: 20819 AN XY: 620258

Gnomad4 AFR exome AF: 0.00643

Gnomad4 AMR exome AF: 0.0240

Gnomad4 ASJ exome AF: 0.0507

Gnomad4 EAS exome AF: 0.0000776

Gnomad4 SAS exome AF: 0.0269

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.0321

Gnomad4 OTH exome AF: 0.0331

GnomAD4 genome AF: 0.0368 AC: 5605 AN: 152254 Hom.: 177 Cov.: 32 AF XY: 0.0401 AC XY: 2987 AN XY: 74432

Gnomad4 AFR AF: 0.00871

Gnomad4 AMR AF: 0.0316

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0312

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0401 Hom.: 19

Bravo AF: 0.0295

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11592502; hg19: chr10-94968748;