rs2890930

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.10861806A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;