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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.489 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

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.471

Alfa AF: 0.448 Hom.: 21553

Bravo AF: 0.492

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6021460; hg19: chr20-50426860;