chr18-60093534-A-G

Variant names:

• chr18-60093534-A-G
• rs9948303

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 0.0928 in 152,252 control chromosomes in the GnomAD database, including 695 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 0.093 (695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14125 AN: 152134 Hom.: 694 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0928 AC: 14133 AN: 152252 Hom.: 695 Cov.: 32 AF XY: 0.0921 AC XY: 6854 AN XY: 74452

African (AFR) AF: 0.129 AC: 5350 AN: 41544

American (AMR) AF: 0.102 AC: 1555 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3468

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5186

South Asian (SAS) AF: 0.0550 AC: 265 AN: 4822

European-Finnish (FIN) AF: 0.0943 AC: 1001 AN: 10610

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0818 AC: 5562 AN: 68016

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0835 Hom.: 1031

Bravo AF: 0.0938

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.75
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9948303; hg19: chr18-57760766;