rs9409287

Variant names:

• chr9-126242115-G-T
• rs9409287

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 0.304 in 145,286 control chromosomes in the GnomAD database, including 8,030 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 0.30 (8030 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 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: 0.304 AC: 44199 AN: 145182 Hom.: 8026 Cov.: 26

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.304 AC: 44220 AN: 145286 Hom.: 8030 Cov.: 26 AF XY: 0.305 AC XY: 21345 AN XY: 70070

African (AFR) AF: 0.123 AC: 4984 AN: 40392

American (AMR) AF: 0.239 AC: 3427 AN: 14364

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1466 AN: 3404

East Asian (EAS) AF: 0.316 AC: 1552 AN: 4904

South Asian (SAS) AF: 0.472 AC: 2079 AN: 4400

European-Finnish (FIN) AF: 0.435 AC: 3719 AN: 8544

Middle Eastern (MID) AF: 0.360 AC: 103 AN: 286

European-Non Finnish (NFE) AF: 0.394 AC: 26043 AN: 66100

Other (OTH) AF: 0.285 AC: 576 AN: 2020

Alfa AF: 0.382 Hom.: 3562

Bravo AF: 0.290

Asia WGS AF: 0.394 AC: 1365 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.15
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs9409287; hg19: chr9-129004394;