rs6045592

Variant names:

• chr20-18768883-C-A
• rs6045592

Your query was ambiguous. Multiple possible variants found:

• chr20-18768883-C-A
• chr20-18768883-C-G

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 0.392 in 151,776 control chromosomes in the GnomAD database, including 11,888 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 0.39 (11888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59500 AN: 151658 Hom.: 11879 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.392 AC: 59554 AN: 151776 Hom.: 11888 Cov.: 32 AF XY: 0.389 AC XY: 28841 AN XY: 74150

African (AFR) AF: 0.305 AC: 12634 AN: 41380

American (AMR) AF: 0.385 AC: 5885 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1934 AN: 3460

East Asian (EAS) AF: 0.417 AC: 2144 AN: 5146

South Asian (SAS) AF: 0.340 AC: 1639 AN: 4816

European-Finnish (FIN) AF: 0.404 AC: 4232 AN: 10484

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29615 AN: 67912

Other (OTH) AF: 0.441 AC: 930 AN: 2108

Alfa AF: 0.294 Hom.: 802

Bravo AF: 0.388

Asia WGS AF: 0.406 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6045592; hg19: chr20-18749527;