18-22591091-A-G

Variant names:

• chr18-22591091-A-G
• rs4330012

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 0.674 in 151,972 control chromosomes in the GnomAD database, including 34,828 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 0.67 (34828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102436 AN: 151854 Hom.: 34811 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.674 AC: 102488 AN: 151972 Hom.: 34828 Cov.: 32 AF XY: 0.671 AC XY: 49818 AN XY: 74260

African (AFR) AF: 0.686 AC: 28410 AN: 41444

American (AMR) AF: 0.533 AC: 8151 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2316 AN: 3470

East Asian (EAS) AF: 0.772 AC: 3977 AN: 5154

South Asian (SAS) AF: 0.661 AC: 3183 AN: 4818

European-Finnish (FIN) AF: 0.691 AC: 7281 AN: 10536

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46945 AN: 67954

Other (OTH) AF: 0.651 AC: 1374 AN: 2110

Alfa AF: 0.659 Hom.: 16402

Bravo AF: 0.664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4330012; hg19: chr18-20171054;