rs6082986

Variant names:

• chr20-23043282-A-G
• rs6082986

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 0.337 in 152,180 control chromosomes in the GnomAD database, including 8,861 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 0.34 (8861 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 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: 0.337 AC: 51212 AN: 152062 Hom.: 8867 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.337 AC: 51225 AN: 152180 Hom.: 8861 Cov.: 33 AF XY: 0.339 AC XY: 25242 AN XY: 74406

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.354

Alfa AF: 0.335 Hom.: 1691

Bravo AF: 0.327

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6082986; hg19: chr20-23023919;