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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.821 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

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.833

Alfa AF: 0.804 Hom.: 66534

Bravo AF: 0.830

Asia WGS AF: 0.943 AC: 3277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs486633; hg19: chr18-565760;