rs6028068

Variant names:

• chr20-61195491-T-C
• rs6028068

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 0.122 in 152,206 control chromosomes in the GnomAD database, including 1,374 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 0.12 (1374 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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: 0.122 AC: 18544 AN: 152088 Hom.: 1365 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.122 AC: 18581 AN: 152206 Hom.: 1374 Cov.: 33 AF XY: 0.122 AC XY: 9104 AN XY: 74410

African (AFR) AF: 0.171 AC: 7098 AN: 41520

American (AMR) AF: 0.179 AC: 2739 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3472

East Asian (EAS) AF: 0.122 AC: 631 AN: 5164

South Asian (SAS) AF: 0.105 AC: 507 AN: 4830

European-Finnish (FIN) AF: 0.104 AC: 1099 AN: 10596

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0808 AC: 5497 AN: 68010

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.104 Hom.: 793

Bravo AF: 0.132

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.37
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs6028068; hg19: chr20-59770547;