18-53906430-G-A

Variant names:

• chr18-53906430-G-A
• rs7239408

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 0.271 in 151,864 control chromosomes in the GnomAD database, including 6,070 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 0.27 (6070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.271 AC: 41147 AN: 151746 Hom.: 6060 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0489

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.271 AC: 41180 AN: 151864 Hom.: 6070 Cov.: 32 AF XY: 0.268 AC XY: 19870 AN XY: 74172

African (AFR) AF: 0.378 AC: 15664 AN: 41420

American (AMR) AF: 0.203 AC: 3100 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3466

East Asian (EAS) AF: 0.0490 AC: 253 AN: 5166

South Asian (SAS) AF: 0.208 AC: 997 AN: 4798

European-Finnish (FIN) AF: 0.247 AC: 2606 AN: 10530

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16579 AN: 67934

Other (OTH) AF: 0.260 AC: 549 AN: 2108

Alfa AF: 0.250 Hom.: 13771

Bravo AF: 0.271

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.65
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7239408; hg19: chr18-51432800;