chr9-101860586-G-A

Variant names:

• chr9-101860586-G-A
• rs10989661

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 0.216 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.181 AC: 7512 AN: 41502

American (AMR) AF: 0.195 AC: 2981 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3472

East Asian (EAS) AF: 0.146 AC: 754 AN: 5166

South Asian (SAS) AF: 0.141 AC: 680 AN: 4826

European-Finnish (FIN) AF: 0.224 AC: 2369 AN: 10586

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17032 AN: 67998

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.239 Hom.: 19829

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

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