rs2150864

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;