rs6021460

Variant names:

• chr20-51810321-A-G
• rs6021460

Your query was ambiguous. Multiple possible variants found:

• chr20-51810321-A-G
• chr20-51810321-A-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 0.489 in 151,950 control chromosomes in the GnomAD database, including 18,944 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 0.49 (18944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 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: 0.489 AC: 74200 AN: 151832 Hom.: 18914 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.489 AC: 74295 AN: 151950 Hom.: 18944 Cov.: 32 AF XY: 0.486 AC XY: 36087 AN XY: 74278

African (AFR) AF: 0.641 AC: 26555 AN: 41436

American (AMR) AF: 0.415 AC: 6335 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1893 AN: 5160

South Asian (SAS) AF: 0.375 AC: 1802 AN: 4804

European-Finnish (FIN) AF: 0.418 AC: 4406 AN: 10548

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30263 AN: 67952

Other (OTH) AF: 0.471 AC: 995 AN: 2112

Alfa AF: 0.462 Hom.: 35810

Bravo AF: 0.492

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.35
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6021460; hg19: chr20-50426860;