rs486633

Variant names:

• chr18-565760-A-C
• rs486633

Your query was ambiguous. Multiple possible variants found:

• chr18-565760-A-C
• chr18-565760-A-G
• chr18-565760-A-T

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 0.821 in 152,088 control chromosomes in the GnomAD database, including 51,445 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 0.82 (51445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124730 AN: 151970 Hom.: 51399 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.821 AC: 124834 AN: 152088 Hom.: 51445 Cov.: 32 AF XY: 0.824 AC XY: 61244 AN XY: 74336

African (AFR) AF: 0.838 AC: 34761 AN: 41496

American (AMR) AF: 0.882 AC: 13477 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2952 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5136 AN: 5154

South Asian (SAS) AF: 0.889 AC: 4287 AN: 4824

European-Finnish (FIN) AF: 0.769 AC: 8133 AN: 10570

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53397 AN: 67976

Other (OTH) AF: 0.833 AC: 1759 AN: 2112

Alfa AF: 0.806 Hom.: 84772

Bravo AF: 0.830

Asia WGS AF: 0.943 AC: 3277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.32
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs486633; hg19: chr18-565760;