rs228199

Positions:

• chr20-48169863-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;