chr9-101467513-G-A

Variant names:

• chr9-101467513-G-A
• rs882809

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.882 AC: 36644 AN: 41530

American (AMR) AF: 0.709 AC: 10821 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1973 AN: 3468

East Asian (EAS) AF: 0.884 AC: 4572 AN: 5172

South Asian (SAS) AF: 0.799 AC: 3842 AN: 4808

European-Finnish (FIN) AF: 0.670 AC: 7054 AN: 10536

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.614 AC: 41704 AN: 67936

Other (OTH) AF: 0.687 AC: 1450 AN: 2112

Alfa AF: 0.644 Hom.: 18829

Bravo AF: 0.723

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs882809; hg19: chr9-104229795;