rs2028455

Positions:

• chr18-50439635-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;