rs6023683

Variant names:

• chr20-54892802-C-T
• rs6023683

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 0.111 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.297 AC: 12292 AN: 41410

American (AMR) AF: 0.0658 AC: 1006 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0505 AC: 175 AN: 3468

East Asian (EAS) AF: 0.0236 AC: 122 AN: 5172

South Asian (SAS) AF: 0.0993 AC: 479 AN: 4824

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10602

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0321 AC: 2184 AN: 68008

Other (OTH) AF: 0.104 AC: 220 AN: 2108

Alfa AF: 0.0680 Hom.: 325

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6023683; hg19: chr20-53509341;