chr18-28193052-C-T

Variant names:

• chr18-28193052-C-T
• rs4800843

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 0.489 in 151,622 control chromosomes in the GnomAD database, including 20,053 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 (20053 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 2 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 = 0.6 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74060 AN: 151504 Hom.: 20058 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.489 AC: 74071 AN: 151622 Hom.: 20053 Cov.: 30 AF XY: 0.491 AC XY: 36411 AN XY: 74082

African (AFR) AF: 0.227 AC: 9376 AN: 41380

American (AMR) AF: 0.538 AC: 8195 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2331 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2701 AN: 5104

South Asian (SAS) AF: 0.586 AC: 2812 AN: 4802

European-Finnish (FIN) AF: 0.543 AC: 5688 AN: 10468

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 41071 AN: 67870

Other (OTH) AF: 0.553 AC: 1162 AN: 2102

Alfa AF: 0.518 Hom.: 2436

Bravo AF: 0.477

Asia WGS AF: 0.510 AC: 1775 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	0.23
DANN	Benign	0.37
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4800843; hg19: chr18-25773016;