rs7069060

Variant names:

• chr10-12281465-A-G
• rs7069060

Your query was ambiguous. Multiple possible variants found:

• chr10-12281465-A-G
• chr10-12281465-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.267 in 151,772 control chromosomes in the GnomAD database, including 5,569 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 0.27 (5569 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40483 AN: 151654 Hom.: 5557 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.250

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.267 AC: 40523 AN: 151772 Hom.: 5569 Cov.: 31 AF XY: 0.270 AC XY: 20037 AN XY: 74138

African (AFR) AF: 0.264 AC: 10945 AN: 41418

American (AMR) AF: 0.223 AC: 3391 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1141 AN: 3458

East Asian (EAS) AF: 0.253 AC: 1301 AN: 5148

South Asian (SAS) AF: 0.326 AC: 1570 AN: 4816

European-Finnish (FIN) AF: 0.362 AC: 3786 AN: 10472

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17601 AN: 67948

Other (OTH) AF: 0.253 AC: 533 AN: 2110

Alfa AF: 0.256 Hom.: 10428

Bravo AF: 0.255

Asia WGS AF: 0.267 AC: 929 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	1.5
DANN	Benign	0.50
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7069060; hg19: chr10-12323464;