10-93208991-C-T

Variant names:

• chr10-93208991-C-T
• rs11592502
• ENST00000420392.1:n.352G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ENSG00000296225 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 177 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XRCC6P1		n.93208991C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XRCC6P1	ENST00000420392.1	n.352G>A		non_coding_transcript_exon_variant	Exon 2 of 4	6
ENSG00000296225	ENST00000737465.1	n.655-1377G>A		intron_variant	Intron 3 of 3
ENSG00000296225	ENST00000737466.1	n.420-1377G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.00643 AC: 187 AN: 29094

American (AMR) AF: 0.0240 AC: 1066 AN: 44368

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 1249 AN: 24648

East Asian (EAS) AF: 0.0000776 AC: 3 AN: 38674

South Asian (SAS) AF: 0.0269 AC: 2182 AN: 81084

European-Finnish (FIN) AF: 0.100 AC: 5338 AN: 53272

Middle Eastern (MID) AF: 0.0512 AC: 187 AN: 3652

European-Non Finnish (NFE) AF: 0.0321 AC: 28889 AN: 898598

Other (OTH) AF: 0.0331 AC: 1737 AN: 52516

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

African (AFR) AF: 0.00871 AC: 362 AN: 41556

American (AMR) AF: 0.0316 AC: 483 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0312 AC: 150 AN: 4810

European-Finnish (FIN) AF: 0.112 AC: 1184 AN: 10604

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0462 AC: 3141 AN: 68022

Other (OTH) AF: 0.0355 AC: 75 AN: 2110

Alfa AF: 0.0390 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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11592502; hg19: chr10-94968748;