rs2890930

Variant names:

• chr9-10861806-A-C
• rs2890930

Your query was ambiguous. Multiple possible variants found:

• chr9-10861806-A-C
• chr9-10861806-A-G

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 0.0834 in 151,674 control chromosomes in the GnomAD database, including 780 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 0.083 (780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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: 0.0834 AC: 12644 AN: 151556 Hom.: 778 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.0711

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

GnomAD4 genome AF: 0.0834 AC: 12644 AN: 151674 Hom.: 780 Cov.: 32 AF XY: 0.0893 AC XY: 6621 AN XY: 74110

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.0983

Gnomad4 OTH AF: 0.0732

Alfa AF: 0.0816 Hom.: 370

Bravo AF: 0.0685

Asia WGS AF: 0.205 AC: 704 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.62
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2890930; hg19: chr9-10861806; COSMIC: COSV69446745;