rs6054633

Variant names:

• chr20-6964719-G-A
• rs6054633

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 0.44 in 151,954 control chromosomes in the GnomAD database, including 16,461 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 0.44 (16461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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: 0.440 AC: 66779 AN: 151836 Hom.: 16468 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.440 AC: 66788 AN: 151954 Hom.: 16461 Cov.: 32 AF XY: 0.447 AC XY: 33221 AN XY: 74240

African (AFR) AF: 0.209 AC: 8689 AN: 41478

American (AMR) AF: 0.567 AC: 8647 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1849 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3697 AN: 5130

South Asian (SAS) AF: 0.482 AC: 2322 AN: 4818

European-Finnish (FIN) AF: 0.542 AC: 5718 AN: 10550

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.505 AC: 34329 AN: 67954

Other (OTH) AF: 0.435 AC: 916 AN: 2108

Alfa AF: 0.490 Hom.: 30438

Bravo AF: 0.432

Asia WGS AF: 0.537 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.088
DANN	Benign	0.33
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6054633; hg19: chr20-6945366;