rs12069719

Variant names:

• chr1-26085427-A-G
• rs12069719

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.346 AC: 14296 AN: 41364

American (AMR) AF: 0.153 AC: 2326 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.126 AC: 648 AN: 5144

South Asian (SAS) AF: 0.0716 AC: 344 AN: 4804

European-Finnish (FIN) AF: 0.147 AC: 1548 AN: 10552

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11696 AN: 67954

Other (OTH) AF: 0.220 AC: 463 AN: 2100

Alfa AF: 0.188 Hom.: 9418

Bravo AF: 0.222

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12069719; hg19: chr1-26411918;