rs7089861

Variant names:

• chr10-6068363-C-G
• rs7089861

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 0.293 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.375 AC: 15093 AN: 40256

American (AMR) AF: 0.313 AC: 4673 AN: 14946

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 789 AN: 3452

East Asian (EAS) AF: 0.220 AC: 1124 AN: 5108

South Asian (SAS) AF: 0.207 AC: 966 AN: 4672

European-Finnish (FIN) AF: 0.218 AC: 2114 AN: 9710

Middle Eastern (MID) AF: 0.245 AC: 71 AN: 290

European-Non Finnish (NFE) AF: 0.268 AC: 18078 AN: 67436

Other (OTH) AF: 0.283 AC: 585 AN: 2066

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7089861; hg19: chr10-6110326;