rs12069004

Variant names:

• chr1-208528320-C-T
• rs12069004

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0172 AC: 716 AN: 41570

American (AMR) AF: 0.0822 AC: 1258 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2196 AN: 5172

South Asian (SAS) AF: 0.140 AC: 674 AN: 4812

European-Finnish (FIN) AF: 0.0780 AC: 827 AN: 10600

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0704 AC: 4786 AN: 68008

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0659 Hom.: 545

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs12069004; hg19: chr1-208701665;