chr18-4539085-G-T

Variant names:

• chr18-4539085-G-T
• rs7228133

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 0.176 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.192 AC: 7952 AN: 41470

American (AMR) AF: 0.197 AC: 3005 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1169 AN: 5162

South Asian (SAS) AF: 0.194 AC: 935 AN: 4814

European-Finnish (FIN) AF: 0.187 AC: 1971 AN: 10536

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10743 AN: 67956

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.160 Hom.: 5734

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
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs7228133; hg19: chr18-4539085;