chr20-41850863-G-A

Variant names:

• chr20-41850863-G-A
• rs2866823

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 0.479 in 151,984 control chromosomes in the GnomAD database, including 17,892 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 0.48 (17892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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: 0.479 AC: 72761 AN: 151866 Hom.: 17849 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.479 AC: 72857 AN: 151984 Hom.: 17892 Cov.: 32 AF XY: 0.490 AC XY: 36371 AN XY: 74276

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.514

Alfa AF: 0.444 Hom.: 14076

Bravo AF: 0.473

Asia WGS AF: 0.703 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2866823; hg19: chr20-40479503;