9-8109693-T-G

Variant names:

• chr9-8109693-T-G
• rs12346254

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.319

Alfa AF: 0.288 Hom.: 5796

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12346254; hg19: chr9-8109693;