chr18-28283384-C-T

Position:

• chr18-28283384-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 0.343 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.381

Alfa AF: 0.352 Hom.: 1600

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1548755; hg19: chr18-25863348;