rs6020157

chr20-49975221-G-A

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 0.282 in 151,582 control chromosomes in the GnomAD database, including 7,722 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 0.28 (7722 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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: 0.282 AC: 42683 AN: 151470 Hom.: 7706 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.282 AC: 42745 AN: 151582 Hom.: 7722 Cov.: 31 AF XY: 0.277 AC XY: 20503 AN XY: 74024

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.289

Alfa AF: 0.198 Hom.: 4520

Bravo AF: 0.307

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.9
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6020157; hg19: chr20-48591758;