chr18-28858890-A-G

Variant names:

• chr18-28858890-A-G
• rs485916

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 0.587 in 151,982 control chromosomes in the GnomAD database, including 27,117 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 0.59 (27117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.586 AC: 89064 AN: 151864 Hom.: 27082 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.587 AC: 89154 AN: 151982 Hom.: 27117 Cov.: 31 AF XY: 0.589 AC XY: 43761 AN XY: 74280

African (AFR) AF: 0.738 AC: 30581 AN: 41456

American (AMR) AF: 0.583 AC: 8907 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3953 AN: 5158

South Asian (SAS) AF: 0.604 AC: 2908 AN: 4818

European-Finnish (FIN) AF: 0.532 AC: 5619 AN: 10560

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33994 AN: 67936

Other (OTH) AF: 0.529 AC: 1114 AN: 2104

Alfa AF: 0.509 Hom.: 30717

Bravo AF: 0.594

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.27
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs485916; hg19: chr18-26438855;