chr18-56552746-A-G

Variant names:

• chr18-56552746-A-G
• rs683366

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 0.719 in 152,086 control chromosomes in the GnomAD database, including 39,694 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 0.72 (39694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109295 AN: 151968 Hom.: 39648 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.719 AC: 109395 AN: 152086 Hom.: 39694 Cov.: 31 AF XY: 0.719 AC XY: 53443 AN XY: 74360

African (AFR) AF: 0.638 AC: 26432 AN: 41446

American (AMR) AF: 0.764 AC: 11682 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3055 AN: 3470

East Asian (EAS) AF: 0.843 AC: 4367 AN: 5178

South Asian (SAS) AF: 0.686 AC: 3307 AN: 4818

European-Finnish (FIN) AF: 0.684 AC: 7239 AN: 10584

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50858 AN: 67986

Other (OTH) AF: 0.743 AC: 1567 AN: 2110

Alfa AF: 0.712 Hom.: 5500

Bravo AF: 0.723

Asia WGS AF: 0.790 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.25
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs683366; hg19: chr18-54219977;