rs12069004

Variant names:

• chr1-208528320-C-T
• rs12069004

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0712 in 152,260 control chromosomes in the GnomAD database, including 808 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 0.071 (808 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.0711 AC: 10824 AN: 152142 Hom.: 805 Cov.: 33

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0712 AC: 10838 AN: 152260 Hom.: 808 Cov.: 33 AF XY: 0.0744 AC XY: 5542 AN XY: 74446

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0780

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0671 Hom.: 444

Bravo AF: 0.0713

Asia WGS AF: 0.260 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	15
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12069004; hg19: chr1-208701665;