9-107391866-A-G

Variant names:

• chr9-107391866-A-G
• rs12343115

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 0.0854 in 152,254 control chromosomes in the GnomAD database, including 1,377 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 0.085 (1377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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: 0.0852 AC: 12965 AN: 152136 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.00829

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0854 AC: 13006 AN: 152254 Hom.: 1377 Cov.: 32 AF XY: 0.0859 AC XY: 6394 AN XY: 74442

African (AFR) AF: 0.247 AC: 10242 AN: 41502

American (AMR) AF: 0.0461 AC: 705 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3470

East Asian (EAS) AF: 0.0530 AC: 275 AN: 5190

South Asian (SAS) AF: 0.140 AC: 676 AN: 4824

European-Finnish (FIN) AF: 0.00829 AC: 88 AN: 10620

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0106 AC: 720 AN: 68036

Other (OTH) AF: 0.0671 AC: 142 AN: 2116

Alfa AF: 0.0453 Hom.: 173

Bravo AF: 0.0922

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.25
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12343115; hg19: chr9-110154147;