rs12000567

Variant names:

• chr9-789499-A-C
• rs12000567

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 0.0281 in 151,338 control chromosomes in the GnomAD database, including 121 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 0.028 (121 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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 = 0.0654 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: 0.0281 AC: 4245 AN: 151224 Hom.: 121 Cov.: 26

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0142

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00398

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0169

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

GnomAD4 genome AF: 0.0281 AC: 4249 AN: 151338 Hom.: 121 Cov.: 26 AF XY: 0.0275 AC XY: 2034 AN XY: 73918

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.0142

Gnomad4 ASJ AF: 0.0162

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.00377

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0167

Alfa AF: 0.0220 Hom.: 7

Bravo AF: 0.0294

Asia WGS AF: 0.00635 AC: 22 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	6.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12000567; hg19: chr9-789499;