rs228199

Variant names:

• chr20-48169863-A-G
• rs228199

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 0.628 in 152,204 control chromosomes in the GnomAD database, including 30,832 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 0.63 (30832 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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: 0.628 AC: 95479 AN: 152086 Hom.: 30798 Cov.: 34

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.628 AC: 95570 AN: 152204 Hom.: 30832 Cov.: 34 AF XY: 0.632 AC XY: 47014 AN XY: 74424

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.609

Alfa AF: 0.591 Hom.: 3358

Bravo AF: 0.635

Asia WGS AF: 0.636 AC: 2214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228199; hg19: chr20-46798606;