18-53946823-A-T

Variant names:

• chr18-53946823-A-T
• rs4131468

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 0.145 in 152,242 control chromosomes in the GnomAD database, including 2,782 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 0.15 (2782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.146 AC: 22144 AN: 152124 Hom.: 2779 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.145 AC: 22148 AN: 152242 Hom.: 2782 Cov.: 32 AF XY: 0.158 AC XY: 11730 AN XY: 74432

African (AFR) AF: 0.0306 AC: 1273 AN: 41576

American (AMR) AF: 0.355 AC: 5419 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2304 AN: 5168

South Asian (SAS) AF: 0.325 AC: 1567 AN: 4828

European-Finnish (FIN) AF: 0.212 AC: 2248 AN: 10600

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8398 AN: 68010

Other (OTH) AF: 0.151 AC: 319 AN: 2112

Alfa AF: 0.126 Hom.: 253

Bravo AF: 0.152

Asia WGS AF: 0.353 AC: 1227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.31
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs4131468; hg19: chr18-51473193;