10-93207319-A-G

Variant names:

• chr10-93207319-A-G
• rs7070947
• ENST00000420392.1:n.1343T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-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 rank	MANE	Protein	UniProt
XRCC6P1		n.93207319A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XRCC6P1	ENST00000420392.1	n.1343T>C		non_coding_transcript_exon_variant	Exon 4 of 4	6
ENSG00000296225	ENST00000737465.1	n.950T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000296225	ENST00000737466.1	n.715T>C		non_coding_transcript_exon_variant	Exon 2 of 2

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

African (AFR) AF: 0.496 AC: 11885 AN: 23948

American (AMR) AF: 0.359 AC: 15046 AN: 41856

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 11060 AN: 22300

East Asian (EAS) AF: 0.0637 AC: 2381 AN: 37370

South Asian (SAS) AF: 0.405 AC: 30758 AN: 76012

European-Finnish (FIN) AF: 0.470 AC: 20907 AN: 44470

Middle Eastern (MID) AF: 0.556 AC: 1721 AN: 3096

European-Non Finnish (NFE) AF: 0.580 AC: 405463 AN: 699386

Other (OTH) AF: 0.524 AC: 23221 AN: 44310

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

African (AFR) AF: 0.495 AC: 20498 AN: 41412

American (AMR) AF: 0.471 AC: 7183 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3470

East Asian (EAS) AF: 0.0470 AC: 242 AN: 5146

South Asian (SAS) AF: 0.386 AC: 1853 AN: 4802

European-Finnish (FIN) AF: 0.437 AC: 4590 AN: 10504

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39476 AN: 67966

Other (OTH) AF: 0.533 AC: 1121 AN: 2102

Alfa AF: 0.556 Hom.: 87362

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
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs7070947; hg19: chr10-94967076;