chr18-50439635-C-T

Variant names:

• chr18-50439635-C-T
• rs2028455

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 0.374 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.434 AC: 17986 AN: 41408

American (AMR) AF: 0.437 AC: 6680 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3056 AN: 5152

South Asian (SAS) AF: 0.367 AC: 1764 AN: 4810

European-Finnish (FIN) AF: 0.365 AC: 3851 AN: 10560

Middle Eastern (MID) AF: 0.317 AC: 92 AN: 290

European-Non Finnish (NFE) AF: 0.311 AC: 21135 AN: 67930

Other (OTH) AF: 0.353 AC: 742 AN: 2104

Alfa AF: 0.332 Hom.: 8775

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
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2028455; hg19: chr18-47966005;