rs12000794

Variant names:

• chr9-100395233-C-A
• rs12000794

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 0.16 in 152,154 control chromosomes in the GnomAD database, including 2,030 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 0.16 (2030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 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: 0.159 AC: 24227 AN: 152036 Hom.: 2019 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.160 AC: 24284 AN: 152154 Hom.: 2030 Cov.: 31 AF XY: 0.155 AC XY: 11519 AN XY: 74380

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.154

Alfa AF: 0.169 Hom.: 4675

Bravo AF: 0.158

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12000794; hg19: chr9-103157515;