rs211833

chr20-39850639-A-Gchr20-39850639-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;