rs9662589

Variant names:

• chr1-232141865-A-C
• rs9662589

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 0.324 in 152,088 control chromosomes in the GnomAD database, including 9,752 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 0.32 (9752 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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: 0.324 AC: 49225 AN: 151970 Hom.: 9726 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.324 AC: 49311 AN: 152088 Hom.: 9752 Cov.: 33 AF XY: 0.320 AC XY: 23780 AN XY: 74354

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.283

Alfa AF: 0.252 Hom.: 2795

Bravo AF: 0.338

Asia WGS AF: 0.306 AC: 1065 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9662589; hg19: chr1-232277611;