rs6023683

Variant names:

• chr20-54892802-C-T
• rs6023683

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 0.111 in 152,096 control chromosomes in the GnomAD database, including 1,983 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 0.11 (1983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.111 AC: 16811 AN: 151978 Hom.: 1977 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0321

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.111 AC: 16844 AN: 152096 Hom.: 1983 Cov.: 32 AF XY: 0.109 AC XY: 8098 AN XY: 74370

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.0658

Gnomad4 ASJ AF: 0.0505

Gnomad4 EAS AF: 0.0236

Gnomad4 SAS AF: 0.0993

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0321

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0633 Hom.: 167

Bravo AF: 0.120

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6023683; hg19: chr20-53509341;