rs10989661

chr9-101860586-G-A

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 0.216 in 152,122 control chromosomes in the GnomAD database, including 3,668 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 0.22 (3668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 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: 0.216 AC: 32820 AN: 152004 Hom.: 3660 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.216 AC: 32835 AN: 152122 Hom.: 3668 Cov.: 32 AF XY: 0.213 AC XY: 15868 AN XY: 74372

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.230

Alfa AF: 0.242 Hom.: 10152

Bravo AF: 0.214

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.18
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10989661; hg19: chr9-104622868; COSMIC: COSV60382710;