18-53994250-G-A

Variant names:

• chr18-53994250-G-A
• rs9304456

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.207 in 152,084 control chromosomes in the GnomAD database, including 3,433 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 0.21 (3433 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.207 AC: 31436 AN: 151966 Hom.: 3429 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.207 AC: 31446 AN: 152084 Hom.: 3433 Cov.: 33 AF XY: 0.204 AC XY: 15176 AN XY: 74344

African (AFR) AF: 0.209 AC: 8652 AN: 41460

American (AMR) AF: 0.145 AC: 2217 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3470

East Asian (EAS) AF: 0.0499 AC: 259 AN: 5186

South Asian (SAS) AF: 0.138 AC: 663 AN: 4816

European-Finnish (FIN) AF: 0.233 AC: 2455 AN: 10554

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15795 AN: 67990

Other (OTH) AF: 0.189 AC: 399 AN: 2114

Alfa AF: 0.218 Hom.: 2152

Bravo AF: 0.201

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.53
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs9304456; hg19: chr18-51520620;