rs10811469

Variant names:

• chr9-21086341-A-G
• rs10811469

Your query was ambiguous. Multiple possible variants found:

• chr9-21086341-A-G
• chr9-21086341-A-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 0.118 in 151,850 control chromosomes in the GnomAD database, including 1,146 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 0.12 (1146 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 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: 0.118 AC: 17916 AN: 151732 Hom.: 1144 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0540

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.118 AC: 17922 AN: 151850 Hom.: 1146 Cov.: 31 AF XY: 0.117 AC XY: 8653 AN XY: 74204

African (AFR) AF: 0.122 AC: 5067 AN: 41448

American (AMR) AF: 0.0829 AC: 1266 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1031 AN: 5174

South Asian (SAS) AF: 0.165 AC: 796 AN: 4818

European-Finnish (FIN) AF: 0.0540 AC: 566 AN: 10472

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8068 AN: 67888

Other (OTH) AF: 0.132 AC: 278 AN: 2106

Alfa AF: 0.0577 Hom.: 67

Bravo AF: 0.121

Asia WGS AF: 0.195 AC: 675 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10811469; hg19: chr9-21086340; COSMIC: COSV69450610;