chr18-41093013-G-A

Variant names:

• chr18-41093013-G-A
• rs4890286

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 0.927 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.927 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

African (AFR) AF: 0.972 AC: 40291 AN: 41454

American (AMR) AF: 0.847 AC: 12794 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3321 AN: 3450

East Asian (EAS) AF: 0.511 AC: 2589 AN: 5068

South Asian (SAS) AF: 0.831 AC: 4007 AN: 4820

European-Finnish (FIN) AF: 0.974 AC: 10344 AN: 10620

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.946 AC: 63912 AN: 67534

Other (OTH) AF: 0.927 AC: 1951 AN: 2104

Alfa AF: 0.930 Hom.: 43758

Bravo AF: 0.916

Asia WGS AF: 0.741 AC: 2580 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.25
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4890286; hg19: chr18-38672977;