chr9-8109693-T-G

Variant names:

• chr9-8109693-T-G
• rs12346254

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 0.314 in 151,664 control chromosomes in the GnomAD database, including 7,617 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 0.31 (7617 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.314 AC: 47631 AN: 151544 Hom.: 7617 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.314 AC: 47658 AN: 151664 Hom.: 7617 Cov.: 31 AF XY: 0.309 AC XY: 22883 AN XY: 74100

African (AFR) AF: 0.369 AC: 15257 AN: 41332

American (AMR) AF: 0.340 AC: 5174 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3464

East Asian (EAS) AF: 0.276 AC: 1404 AN: 5084

South Asian (SAS) AF: 0.219 AC: 1053 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2476 AN: 10562

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19899 AN: 67896

Other (OTH) AF: 0.319 AC: 673 AN: 2110

Alfa AF: 0.292 Hom.: 7203

Bravo AF: 0.326

Asia WGS AF: 0.246 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs12346254; hg19: chr9-8109693;