rs12343206

Positions:

• chr9-124421788-A-G

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 0.525 in 152,108 control chromosomes in the GnomAD database, including 21,747 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 0.52 (21747 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.124421788A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79770 AN: 151990 Hom.: 21733 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.525 AC: 79810 AN: 152108 Hom.: 21747 Cov.: 33 AF XY: 0.523 AC XY: 38892 AN XY: 74378

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.545

Alfa AF: 0.582 Hom.: 45391

Bravo AF: 0.506

Asia WGS AF: 0.389 AC: 1356 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	2.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12343206; hg19: chr9-127184067;