18-28455130-A-T

Variant names:

• chr18-28455130-A-T
• rs4800876

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.251 in 152,148 control chromosomes in the GnomAD database, including 5,013 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 0.25 (5013 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38239 AN: 152030 Hom.: 5019 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.251 AC: 38239 AN: 152148 Hom.: 5013 Cov.: 33 AF XY: 0.253 AC XY: 18813 AN XY: 74386

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.257

Alfa AF: 0.145 Hom.: 280

Bravo AF: 0.241

Asia WGS AF: 0.234 AC: 815 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800876; hg19: chr18-26035094;