rs4890286

Variant names:

• chr18-41093013-G-A
• rs4890286

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 0.927 in 151,368 control chromosomes in the GnomAD database, including 65,677 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 0.93 (65677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 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: 0.927 AC: 140157 AN: 151248 Hom.: 65617 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.927 AC: 140270 AN: 151368 Hom.: 65677 Cov.: 32 AF XY: 0.923 AC XY: 68204 AN XY: 73918

Gnomad4 AFR AF: 0.972

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.927

Alfa AF: 0.944 Hom.: 17247

Bravo AF: 0.916

Asia WGS AF: 0.741 AC: 2580 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4890286; hg19: chr18-38672977;