rs7070947

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 ENST00000737465.1(ENSG00000296225):​n.950T>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: ENSG00000296225 ENST00000737465.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737465.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XRCC6P1	ENST00000420392.1	TSL:6	n.1343T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000296225	ENST00000737465.1		n.950T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000296225	ENST00000737466.1		n.715T>C		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7070947;

hg19: chr10-94967076;