rs6013509

Variant names:

• chr20-52701812-G-A
• rs6013509

Your query was ambiguous. Multiple possible variants found:

• chr20-52701812-G-A
• chr20-52701812-G-C

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 0.3 in 151,856 control chromosomes in the GnomAD database, including 7,439 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 0.30 (7439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679
• Publications: 22 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 (SAS) allele frequency at 95% confidence interval = 0.464 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: 0.299 AC: 45440 AN: 151738 Hom.: 7419 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.300 AC: 45521 AN: 151856 Hom.: 7439 Cov.: 32 AF XY: 0.298 AC XY: 22111 AN XY: 74218

African (AFR) AF: 0.420 AC: 17396 AN: 41370

American (AMR) AF: 0.250 AC: 3817 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1793 AN: 5164

South Asian (SAS) AF: 0.480 AC: 2307 AN: 4802

European-Finnish (FIN) AF: 0.162 AC: 1709 AN: 10532

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16543 AN: 67946

Other (OTH) AF: 0.307 AC: 645 AN: 2104

Alfa AF: 0.263 Hom.: 26065

Bravo AF: 0.301

Asia WGS AF: 0.429 AC: 1491 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	4.3
DANN	Benign	0.85
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6013509; hg19: chr20-51318351;