rs6013509

Positions:

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

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 0.3 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.307

Alfa AF: 0.255 Hom.: 11320

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6013509; hg19: chr20-51318351;