rs6137866

Variant names:

• chr20-23199352-G-A
• rs6137866

Your query was ambiguous. Multiple possible variants found:

• chr20-23199352-G-A
• chr20-23199352-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.135 in 152,156 control chromosomes in the GnomAD database, including 1,629 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 0.14 (1629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 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: 0.135 AC: 20568 AN: 152038 Hom.: 1626 Cov.: 33

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.135 AC: 20581 AN: 152156 Hom.: 1629 Cov.: 33 AF XY: 0.138 AC XY: 10252 AN XY: 74346

African (AFR) AF: 0.0704 AC: 2926 AN: 41556

American (AMR) AF: 0.110 AC: 1675 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1605 AN: 5160

South Asian (SAS) AF: 0.195 AC: 937 AN: 4802

European-Finnish (FIN) AF: 0.167 AC: 1760 AN: 10562

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10460 AN: 67994

Other (OTH) AF: 0.152 AC: 320 AN: 2110

Alfa AF: 0.149 Hom.: 2994

Bravo AF: 0.131

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
DANN	Benign	0.65
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6137866; hg19: chr20-23179989;