rs9288087

Variant names:

• chr2-182867309-G-A
• rs9288087

Your query was ambiguous. Multiple possible variants found:

• chr2-182867309-G-A
• chr2-182867309-G-C

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 0.219 in 152,182 control chromosomes in the GnomAD database, including 4,547 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 (4543 hom., cov: 31)
  • Exomes 𝑓: 0.21 (4 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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: 0.219 AC: 33320 AN: 151968 Hom.: 4536 Cov.: 31

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.208 AC: 20 AN: 96 Hom.: 4 AF XY: 0.188 AC XY: 12 AN XY: 64

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.238

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.219 AC: 33340 AN: 152086 Hom.: 4543 Cov.: 31 AF XY: 0.228 AC XY: 16930 AN XY: 74318

Gnomad4 AFR AF: 0.0775

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.222

Alfa AF: 0.234 Hom.: 584

Bravo AF: 0.203

Asia WGS AF: 0.371 AC: 1289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.6
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9288087; hg19: chr2-183732037;