rs211833

Variant names:

• chr20-39850639-A-G
• rs211833

Your query was ambiguous. Multiple possible variants found:

• chr20-39850639-A-G
• chr20-39850639-A-T

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 0.529 in 152,130 control chromosomes in the GnomAD database, including 21,909 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 0.53 (21909 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 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: 0.529 AC: 80471 AN: 152012 Hom.: 21884 Cov.: 34

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.529 AC: 80547 AN: 152130 Hom.: 21909 Cov.: 34 AF XY: 0.528 AC XY: 39266 AN XY: 74366

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.460

Alfa AF: 0.514 Hom.: 2394

Bravo AF: 0.525

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.97
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs211833; hg19: chr20-38479281;