rs1888223

Variant names:

• chr9-99102692-C-A
• rs1888223

Your query was ambiguous. Multiple possible variants found:

• chr9-99102692-C-A
• chr9-99102692-C-G
• chr9-99102692-C-T

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 0.314 in 152,064 control chromosomes in the GnomAD database, including 7,612 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 0.31 (7612 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -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 = 0.418 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: 0.314 AC: 47684 AN: 151946 Hom.: 7592 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.314 AC: 47753 AN: 152064 Hom.: 7612 Cov.: 33 AF XY: 0.312 AC XY: 23202 AN XY: 74344

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.310

Alfa AF: 0.206 Hom.: 592

Bravo AF: 0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.099
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1888223; hg19: chr9-101864974;