rs2028455

Variant names:

• chr18-50439635-C-T
• rs2028455

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 0.374 in 151,912 control chromosomes in the GnomAD database, including 11,052 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 0.37 (11052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 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: 0.373 AC: 56693 AN: 151794 Hom.: 11027 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.374 AC: 56760 AN: 151912 Hom.: 11052 Cov.: 31 AF XY: 0.381 AC XY: 28254 AN XY: 74226

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.353

Alfa AF: 0.329 Hom.: 3856

Bravo AF: 0.385

Asia WGS AF: 0.463 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2028455; hg19: chr18-47966005;