rs2150864

Variant names:

• chr9-29363267-G-A
• rs2150864

Your query was ambiguous. Multiple possible variants found:

• chr9-29363267-G-A
• chr9-29363267-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 0.667 in 151,922 control chromosomes in the GnomAD database, including 34,132 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 0.67 (34132 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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: 0.667 AC: 101210 AN: 151806 Hom.: 34081 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.667 AC: 101318 AN: 151922 Hom.: 34132 Cov.: 31 AF XY: 0.661 AC XY: 49050 AN XY: 74242

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.657

Alfa AF: 0.646 Hom.: 16939

Bravo AF: 0.670

Asia WGS AF: 0.522 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2150864; hg19: chr9-29363265;