rs9869409

Variant names:

• chr3-180277213-G-A
• rs9869409

Your query was ambiguous. Multiple possible variants found:

• chr3-180277213-G-A
• chr3-180277213-G-C
• chr3-180277213-G-T

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 0.116 in 152,082 control chromosomes in the GnomAD database, including 1,398 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 0.12 (1398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17609 AN: 151964 Hom.: 1396 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.116 AC: 17624 AN: 152082 Hom.: 1398 Cov.: 32 AF XY: 0.114 AC XY: 8485 AN XY: 74354

African (AFR) AF: 0.236 AC: 9777 AN: 41472

American (AMR) AF: 0.0782 AC: 1194 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3468

East Asian (EAS) AF: 0.0178 AC: 92 AN: 5172

South Asian (SAS) AF: 0.166 AC: 801 AN: 4818

European-Finnish (FIN) AF: 0.0505 AC: 535 AN: 10588

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4666 AN: 67984

Other (OTH) AF: 0.106 AC: 223 AN: 2110

Alfa AF: 0.0816 Hom.: 411

Bravo AF: 0.121

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs9869409; hg19: chr3-179995001;