rs6090314

Variant names:

• chr20-63226200-G-A
• rs6090314

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 0.165 in 152,126 control chromosomes in the GnomAD database, including 2,251 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 (2251 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.165 AC: 25106 AN: 152008 Hom.: 2253 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.165 AC: 25107 AN: 152126 Hom.: 2251 Cov.: 33 AF XY: 0.167 AC XY: 12392 AN XY: 74360

African (AFR) AF: 0.142 AC: 5894 AN: 41514

American (AMR) AF: 0.162 AC: 2475 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1835 AN: 5158

South Asian (SAS) AF: 0.193 AC: 931 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1759 AN: 10566

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10949 AN: 67978

Other (OTH) AF: 0.190 AC: 402 AN: 2116

Alfa AF: 0.165 Hom.: 3901

Bravo AF: 0.165

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.81
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6090314; hg19: chr20-61857552;