18-51284217-G-A

Variant names:

• chr18-51284217-G-A
• rs4456603

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 0.855 in 151,896 control chromosomes in the GnomAD database, including 56,129 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 0.86 (56129 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129806 AN: 151778 Hom.: 56102 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.855 AC: 129882 AN: 151896 Hom.: 56129 Cov.: 30 AF XY: 0.851 AC XY: 63180 AN XY: 74224

African (AFR) AF: 0.730 AC: 30213 AN: 41390

American (AMR) AF: 0.852 AC: 12997 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4356 AN: 5162

South Asian (SAS) AF: 0.866 AC: 4168 AN: 4814

European-Finnish (FIN) AF: 0.882 AC: 9262 AN: 10500

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.927 AC: 62991 AN: 67988

Other (OTH) AF: 0.837 AC: 1762 AN: 2106

Alfa AF: 0.899 Hom.: 187376

Bravo AF: 0.847

Asia WGS AF: 0.848 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.21
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4456603; hg19: chr18-48810587;