rs12000567

Positions:

• chr9-789499-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;