rs1883833

chr20-46136819-G-Achr20-46136819-G-C

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 0.3 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

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 (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.300 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

Gnomad4 AFR AF: 0.0977

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.312

Alfa AF: 0.379 Hom.: 15008

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883833; hg19: chr20-44765458;