rs527485

Variant names:

• chr9-22628932-A-G
• rs527485

Your query was ambiguous. Multiple possible variants found:

• chr9-22628932-A-G
• chr9-22628932-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 0.221 in 151,844 control chromosomes in the GnomAD database, including 4,632 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 (4632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 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: 0.221 AC: 33565 AN: 151726 Hom.: 4636 Cov.: 32

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.221 AC: 33564 AN: 151844 Hom.: 4632 Cov.: 32 AF XY: 0.229 AC XY: 16964 AN XY: 74184

African (AFR) AF: 0.0550 AC: 2278 AN: 41436

American (AMR) AF: 0.227 AC: 3451 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2074 AN: 5168

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3870 AN: 10518

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18518 AN: 67912

Other (OTH) AF: 0.209 AC: 442 AN: 2110

Alfa AF: 0.239 Hom.: 886

Bravo AF: 0.206

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs527485; hg19: chr9-22628931;