rs882809

Variant names:

• chr9-101467513-G-A
• rs882809

Your query was ambiguous. Multiple possible variants found:

• chr9-101467513-G-A
• chr9-101467513-G-C
• chr9-101467513-G-T

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 0.716 in 152,038 control chromosomes in the GnomAD database, including 40,185 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 0.72 (40185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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: 0.716 AC: 108807 AN: 151920 Hom.: 40132 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.716 AC: 108922 AN: 152038 Hom.: 40185 Cov.: 32 AF XY: 0.721 AC XY: 53540 AN XY: 74308

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.687

Alfa AF: 0.644 Hom.: 17005

Bravo AF: 0.723

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs882809; hg19: chr9-104229795;