rs6513566

Variant names:

• chr20-61225053-A-C
• rs6513566

Your query was ambiguous. Multiple possible variants found:

• chr20-61225053-A-C
• chr20-61225053-A-G
• chr20-61225053-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 0.605 in 151,980 control chromosomes in the GnomAD database, including 28,527 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 0.61 (28527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.606 AC: 91961 AN: 151862 Hom.: 28525 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.605 AC: 91987 AN: 151980 Hom.: 28527 Cov.: 32 AF XY: 0.606 AC XY: 45013 AN XY: 74248

African (AFR) AF: 0.470 AC: 19450 AN: 41426

American (AMR) AF: 0.602 AC: 9192 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4155 AN: 5174

South Asian (SAS) AF: 0.671 AC: 3223 AN: 4802

European-Finnish (FIN) AF: 0.605 AC: 6374 AN: 10532

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45114 AN: 67982

Other (OTH) AF: 0.598 AC: 1261 AN: 2108

Alfa AF: 0.534 Hom.: 1662

Bravo AF: 0.598

Asia WGS AF: 0.665 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs6513566; hg19: chr20-59800109;