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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0606 AC: 2515 AN: 41478

American (AMR) AF: 0.209 AC: 3196 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1986 AN: 5148

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4816

European-Finnish (FIN) AF: 0.0814 AC: 861 AN: 10578

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0557 AC: 3784 AN: 67992

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0739 Hom.: 1398

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
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs6059594; hg19: chr20-32556777;