rs6021460

chr20-51810321-A-Gchr20-51810321-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;