rs804569

Positions:

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

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 0.903 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.960

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.929

Alfa AF: 0.927 Hom.: 33183

Bravo AF: 0.890

Asia WGS AF: 0.970 AC: 3374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs804569; hg19: chr20-22151652;