rs9287989

Variant names:

• chr2-175853013-T-C
• rs9287989

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 0.494 in 152,008 control chromosomes in the GnomAD database, including 18,655 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 0.49 (18655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 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: 0.494 AC: 74963 AN: 151890 Hom.: 18622 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.494 AC: 75040 AN: 152008 Hom.: 18655 Cov.: 32 AF XY: 0.493 AC XY: 36597 AN XY: 74258

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.501

Alfa AF: 0.483 Hom.: 2356

Bravo AF: 0.490

Asia WGS AF: 0.593 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287989; hg19: chr2-176717741;