chr9-99166869-G-A

Variant names:

• chr9-99166869-G-A
• rs334365

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 0.334 in 151,726 control chromosomes in the GnomAD database, including 8,630 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 0.33 (8630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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: 0.334 AC: 50679 AN: 151608 Hom.: 8614 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.334 AC: 50748 AN: 151726 Hom.: 8630 Cov.: 32 AF XY: 0.333 AC XY: 24683 AN XY: 74138

African (AFR) AF: 0.302 AC: 12504 AN: 41384

American (AMR) AF: 0.330 AC: 5033 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3464

East Asian (EAS) AF: 0.476 AC: 2454 AN: 5154

South Asian (SAS) AF: 0.345 AC: 1662 AN: 4814

European-Finnish (FIN) AF: 0.327 AC: 3431 AN: 10504

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23511 AN: 67850

Other (OTH) AF: 0.342 AC: 720 AN: 2104

Alfa AF: 0.325 Hom.: 1026

Bravo AF: 0.332

Asia WGS AF: 0.411 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.8
DANN	Benign	0.88
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs334365; hg19: chr9-101929151;