chr19-20704424-A-G

Variant names:

• chr19-20704424-A-G
• rs12609807

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 0.629 in 151,750 control chromosomes in the GnomAD database, including 32,852 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 0.63 (32852 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.76 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: 0.630 AC: 95484 AN: 151630 Hom.: 32838 Cov.: 31

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.629 AC: 95513 AN: 151750 Hom.: 32852 Cov.: 31 AF XY: 0.630 AC XY: 46704 AN XY: 74122

African (AFR) AF: 0.329 AC: 13650 AN: 41428

American (AMR) AF: 0.771 AC: 11764 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3135 AN: 5136

South Asian (SAS) AF: 0.683 AC: 3291 AN: 4816

European-Finnish (FIN) AF: 0.728 AC: 7639 AN: 10492

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.762 AC: 51689 AN: 67852

Other (OTH) AF: 0.656 AC: 1382 AN: 2106

Alfa AF: 0.720 Hom.: 23849

Bravo AF: 0.619

Asia WGS AF: 0.631 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.56
DANN	Benign	0.24
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12609807; hg19: chr19-20887230;