18-28283384-C-T

Variant names:

• chr18-28283384-C-T
• rs1548755

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 0.343 in 152,126 control chromosomes in the GnomAD database, including 9,509 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 0.34 (9509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 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: 0.343 AC: 52137 AN: 152008 Hom.: 9509 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.343 AC: 52146 AN: 152126 Hom.: 9509 Cov.: 32 AF XY: 0.344 AC XY: 25547 AN XY: 74360

African (AFR) AF: 0.207 AC: 8607 AN: 41520

American (AMR) AF: 0.364 AC: 5557 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1491 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2316 AN: 5168

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4816

European-Finnish (FIN) AF: 0.336 AC: 3555 AN: 10582

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27149 AN: 67982

Other (OTH) AF: 0.381 AC: 803 AN: 2106

Alfa AF: 0.348 Hom.: 1617

Bravo AF: 0.337

Asia WGS AF: 0.433 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.67
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1548755; hg19: chr18-25863348;