rs7069060

chr10-12281465-A-Gchr10-12281465-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.253

Alfa AF: 0.255 Hom.: 7578

Bravo AF: 0.255

Asia WGS AF: 0.267 AC: 929 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	1.5
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7069060; hg19: chr10-12323464;