rs12069719

Variant names:

• chr1-26085427-A-G
• rs12069719

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 0.213 in 151,830 control chromosomes in the GnomAD database, including 4,012 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 0.21 (4012 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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: 0.212 AC: 32217 AN: 151712 Hom.: 3997 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0726

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.213 AC: 32268 AN: 151830 Hom.: 4012 Cov.: 31 AF XY: 0.206 AC XY: 15294 AN XY: 74196

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0716

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.220

Alfa AF: 0.180 Hom.: 5350

Bravo AF: 0.222

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12069719; hg19: chr1-26411918;