20-61166469-G-A

Variant names:

• chr20-61166469-G-A
• rs17805522

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 0.0992 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.0992 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

African (AFR) AF: 0.119 AC: 4950 AN: 41446

American (AMR) AF: 0.0638 AC: 976 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0590 AC: 205 AN: 3472

East Asian (EAS) AF: 0.0870 AC: 450 AN: 5170

South Asian (SAS) AF: 0.102 AC: 489 AN: 4812

European-Finnish (FIN) AF: 0.0548 AC: 579 AN: 10568

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7079 AN: 67984

Other (OTH) AF: 0.0891 AC: 188 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.51
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs17805522; hg19: chr20-59741525;