18-51167225-A-C

Variant names:

• chr18-51167225-A-C
• rs2282543

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 0.487 in 152,020 control chromosomes in the GnomAD database, including 18,294 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 0.49 (18294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.487 AC: 74001 AN: 151902 Hom.: 18278 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.487 AC: 74068 AN: 152020 Hom.: 18294 Cov.: 32 AF XY: 0.483 AC XY: 35885 AN XY: 74334

African (AFR) AF: 0.424 AC: 17593 AN: 41448

American (AMR) AF: 0.452 AC: 6911 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1842 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2315 AN: 5166

South Asian (SAS) AF: 0.451 AC: 2174 AN: 4824

European-Finnish (FIN) AF: 0.487 AC: 5145 AN: 10554

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36493 AN: 67962

Other (OTH) AF: 0.491 AC: 1037 AN: 2112

Alfa AF: 0.513 Hom.: 38019

Bravo AF: 0.478

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.56
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2282543; hg19: chr18-48693595;