chr18-4539085-G-T

Position:

• chr18-4539085-G-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 0.176 in 152,006 control chromosomes in the GnomAD database, including 2,423 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 0.18 (2423 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 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: 0.176 AC: 26684 AN: 151888 Hom.: 2422 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.176 AC: 26721 AN: 152006 Hom.: 2423 Cov.: 33 AF XY: 0.179 AC XY: 13272 AN XY: 74280

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.163

Alfa AF: 0.154 Hom.: 3077

Bravo AF: 0.176

Asia WGS AF: 0.227 AC: 789 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7228133; hg19: chr18-4539085;