rs7089861

Variant names:

• chr10-6068363-C-G
• rs7089861

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 0.293 in 148,846 control chromosomes in the GnomAD database, including 6,730 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 0.29 (6730 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.293 AC: 43634 AN: 148774 Hom.: 6719 Cov.: 29

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.293 AC: 43662 AN: 148846 Hom.: 6730 Cov.: 29 AF XY: 0.290 AC XY: 20981 AN XY: 72452

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.283

Alfa AF: 0.275 Hom.: 767

Bravo AF: 0.308

Asia WGS AF: 0.239 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7089861; hg19: chr10-6110326;