rs10306109

Variant names:

• chr9-122369352-G-A
• rs10306109

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 0.0783 in 152,252 control chromosomes in the GnomAD database, including 566 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 0.078 (566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 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: 0.0783 AC: 11911 AN: 152134 Hom.: 563 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0743

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0783 AC: 11927 AN: 152252 Hom.: 566 Cov.: 32 AF XY: 0.0786 AC XY: 5852 AN XY: 74440

African (AFR) AF: 0.117 AC: 4846 AN: 41538

American (AMR) AF: 0.0345 AC: 528 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0743 AC: 258 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1505 AN: 10592

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0666 AC: 4528 AN: 68020

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0658 Hom.: 490

Bravo AF: 0.0741

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10306109; hg19: chr9-125131631;