rs10989864

Variant names:

• chr9-102136076-C-A
• rs10989864

Your query was ambiguous. Multiple possible variants found:

• chr9-102136076-C-A
• chr9-102136076-C-G
• chr9-102136076-C-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 0.292 in 151,694 control chromosomes in the GnomAD database, including 7,783 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 (7783 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44368 AN: 151576 Hom.: 7791 Cov.: 30

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.292 AC: 44359 AN: 151694 Hom.: 7783 Cov.: 30 AF XY: 0.292 AC XY: 21634 AN XY: 74098

African (AFR) AF: 0.130 AC: 5369 AN: 41418

American (AMR) AF: 0.264 AC: 4012 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3464

East Asian (EAS) AF: 0.0526 AC: 271 AN: 5150

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4810

European-Finnish (FIN) AF: 0.412 AC: 4302 AN: 10452

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26212 AN: 67866

Other (OTH) AF: 0.314 AC: 662 AN: 2106

Alfa AF: 0.203 Hom.: 574

Bravo AF: 0.273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.27
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs10989864; hg19: chr9-104898358;