rs12343206

Variant names:

• chr9-124421788-A-G
• rs12343206

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 0.525 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 8 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 (NFE) allele frequency at 95% confidence interval = 0.598 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: 0.525 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

African (AFR) AF: 0.404 AC: 16753 AN: 41476

American (AMR) AF: 0.526 AC: 8028 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1642 AN: 5182

South Asian (SAS) AF: 0.398 AC: 1918 AN: 4816

European-Finnish (FIN) AF: 0.640 AC: 6778 AN: 10598

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40975 AN: 67984

Other (OTH) AF: 0.545 AC: 1148 AN: 2106

Alfa AF: 0.575 Hom.: 52556

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
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs12343206; hg19: chr9-127184067;