rs17805522

chr20-61166469-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;