rs6059594

Variant names:

• chr20-33968971-G-A
• rs6059594

Your query was ambiguous. Multiple possible variants found:

• chr20-33968971-G-A
• chr20-33968971-G-C
• chr20-33968971-G-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 0.091 in 152,074 control chromosomes in the GnomAD database, including 1,155 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 0.091 (1155 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 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: 0.0908 AC: 13802 AN: 151954 Hom.: 1143 Cov.: 31

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0557

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0910 AC: 13834 AN: 152074 Hom.: 1155 Cov.: 31 AF XY: 0.0983 AC XY: 7308 AN XY: 74342

Gnomad4 AFR AF: 0.0606

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.0814

Gnomad4 NFE AF: 0.0557

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0641 Hom.: 227

Bravo AF: 0.0995

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6059594; hg19: chr20-32556777;