rs6092090

Variant names:

• chr20-55215117-T-C
• rs6092090

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 0.172 in 152,158 control chromosomes in the GnomAD database, including 2,469 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 0.17 (2469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.29
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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: 0.172 AC: 26145 AN: 152040 Hom.: 2468 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.172 AC: 26142 AN: 152158 Hom.: 2469 Cov.: 32 AF XY: 0.175 AC XY: 12993 AN XY: 74400

African (AFR) AF: 0.157 AC: 6535 AN: 41512

American (AMR) AF: 0.159 AC: 2430 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5186

South Asian (SAS) AF: 0.0983 AC: 475 AN: 4832

European-Finnish (FIN) AF: 0.254 AC: 2691 AN: 10578

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12705 AN: 67984

Other (OTH) AF: 0.189 AC: 400 AN: 2114

Alfa AF: 0.184 Hom.: 4857

Bravo AF: 0.165

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs6092090; hg19: chr20-53831656;