rs9826022

Variant names:

• chr3-185639472-A-G
• rs9826022

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 0.0859 in 152,174 control chromosomes in the GnomAD database, including 821 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 0.086 (821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.0859 AC: 13060 AN: 152056 Hom.: 825 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0859 AC: 13066 AN: 152174 Hom.: 821 Cov.: 32 AF XY: 0.0891 AC XY: 6628 AN XY: 74384

African (AFR) AF: 0.0973 AC: 4038 AN: 41518

American (AMR) AF: 0.0892 AC: 1363 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1194 AN: 5154

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4818

European-Finnish (FIN) AF: 0.0519 AC: 551 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3890 AN: 68000

Other (OTH) AF: 0.0855 AC: 181 AN: 2116

Alfa AF: 0.0653 Hom.: 965

Bravo AF: 0.0821

Asia WGS AF: 0.257 AC: 894 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	3.9
DANN	Benign	0.48
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs9826022; hg19: chr3-185357260;