chr18-28858890-A-G

Position:

• chr18-28858890-A-G

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 0.587 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.586 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

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.529

Alfa AF: 0.507 Hom.: 25726

Bravo AF: 0.594

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs485916; hg19: chr18-26438855;