rs1883833

Variant names:

• chr20-46136819-G-A
• rs1883833

Your query was ambiguous. Multiple possible variants found:

• chr20-46136819-G-A
• chr20-46136819-G-C

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 0.3 in 151,616 control chromosomes in the GnomAD database, including 8,105 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 0.30 (8105 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.300 AC: 45496 AN: 151504 Hom.: 8102 Cov.: 30

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.300 AC: 45506 AN: 151616 Hom.: 8105 Cov.: 30 AF XY: 0.298 AC XY: 22068 AN XY: 74010

African (AFR) AF: 0.0977 AC: 4045 AN: 41382

American (AMR) AF: 0.280 AC: 4269 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1447 AN: 3460

East Asian (EAS) AF: 0.317 AC: 1632 AN: 5150

South Asian (SAS) AF: 0.385 AC: 1852 AN: 4806

European-Finnish (FIN) AF: 0.377 AC: 3919 AN: 10396

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.401 AC: 27189 AN: 67874

Other (OTH) AF: 0.312 AC: 656 AN: 2104

Alfa AF: 0.368 Hom.: 18292

Bravo AF: 0.286

Asia WGS AF: 0.308 AC: 1071 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.68
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1883833; hg19: chr20-44765458;