rs6018089

Variant names:

• chr20-46834668-T-C
• rs6018089

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 0.527 in 149,802 control chromosomes in the GnomAD database, including 22,583 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 0.53 (22583 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 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: 0.527 AC: 78950 AN: 149698 Hom.: 22578 Cov.: 26

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.527 AC: 78973 AN: 149802 Hom.: 22583 Cov.: 26 AF XY: 0.520 AC XY: 38026 AN XY: 73156

African (AFR) AF: 0.364 AC: 14705 AN: 40438

American (AMR) AF: 0.462 AC: 6937 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2267 AN: 3450

East Asian (EAS) AF: 0.0886 AC: 453 AN: 5114

South Asian (SAS) AF: 0.364 AC: 1714 AN: 4714

European-Finnish (FIN) AF: 0.647 AC: 6656 AN: 10294

Middle Eastern (MID) AF: 0.483 AC: 139 AN: 288

European-Non Finnish (NFE) AF: 0.659 AC: 44467 AN: 67510

Other (OTH) AF: 0.522 AC: 1085 AN: 2078

Alfa AF: 0.588 Hom.: 13352

Bravo AF: 0.500

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6018089; hg19: chr20-45463307;