rs17805522

Variant names:

• chr20-61166469-G-A
• rs17805522

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 0.0992 in 152,060 control chromosomes in the GnomAD database, including 818 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 0.099 (818 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0992 AC: 15068 AN: 151944 Hom.: 815 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0891

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

GnomAD4 genome AF: 0.0992 AC: 15087 AN: 152060 Hom.: 818 Cov.: 32 AF XY: 0.0964 AC XY: 7161 AN XY: 74318

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.0590

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0548

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0891

Alfa AF: 0.101 Hom.: 174

Bravo AF: 0.102

Asia WGS AF: 0.0970 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17805522; hg19: chr20-59741525;