rs804569

Variant names:

• chr20-22171014-G-A
• rs804569

Your query was ambiguous. Multiple possible variants found:

• chr20-22171014-G-A
• chr20-22171014-G-C

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 0.903 in 152,088 control chromosomes in the GnomAD database, including 62,282 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 0.90 (62282 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137223 AN: 151970 Hom.: 62254 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.903 AC: 137304 AN: 152088 Hom.: 62282 Cov.: 30 AF XY: 0.904 AC XY: 67197 AN XY: 74336

African (AFR) AF: 0.816 AC: 33845 AN: 41458

American (AMR) AF: 0.853 AC: 13032 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3425 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5119 AN: 5136

South Asian (SAS) AF: 0.973 AC: 4695 AN: 4824

European-Finnish (FIN) AF: 0.960 AC: 10174 AN: 10598

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63958 AN: 68010

Other (OTH) AF: 0.929 AC: 1963 AN: 2112

Alfa AF: 0.924 Hom.: 38621

Bravo AF: 0.890

Asia WGS AF: 0.970 AC: 3374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.35
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs804569; hg19: chr20-22151652;