rs7070947

Positions:

• chr10-93207319-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420392.1(XRCC6P1):​n.1343T>C 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 0.524 in 1,144,614 control chromosomes in the GnomAD database, including 165,382 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 0.51 (20527 hom., cov: 33)
  • Exomes 𝑓: 0.53 (144855 hom.)
• Consequence: XRCC6P1 ENST00000420392.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.47

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XRCC6P1	ENST00000420392.1	n.1343T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77153 AN: 151748 Hom.: 20524 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.530

GnomAD4 exome AF: 0.526 AC: 522442 AN: 992748 Hom.: 144855 Cov.: 14 AF XY: 0.525 AC XY: 269709 AN XY: 513548

Gnomad4 AFR exome AF: 0.496

Gnomad4 AMR exome AF: 0.359

Gnomad4 ASJ exome AF: 0.496

Gnomad4 EAS exome AF: 0.0637

Gnomad4 SAS exome AF: 0.405

Gnomad4 FIN exome AF: 0.470

Gnomad4 NFE exome AF: 0.580

Gnomad4 OTH exome AF: 0.524

GnomAD4 genome AF: 0.508 AC: 77193 AN: 151866 Hom.: 20527 Cov.: 33 AF XY: 0.496 AC XY: 36823 AN XY: 74202

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.533

Alfa AF: 0.566 Hom.: 38342

Bravo AF: 0.505

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7070947; hg19: chr10-94967076;