chr18-22599418-G-A

Variant names:

• chr18-22599418-G-A
• rs11662668

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 0.383 in 152,002 control chromosomes in the GnomAD database, including 13,598 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 0.38 (13598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 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: 0.383 AC: 58199 AN: 151884 Hom.: 13600 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.383 AC: 58197 AN: 152002 Hom.: 13598 Cov.: 32 AF XY: 0.384 AC XY: 28532 AN XY: 74284

African (AFR) AF: 0.120 AC: 4993 AN: 41488

American (AMR) AF: 0.289 AC: 4412 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2370 AN: 5146

South Asian (SAS) AF: 0.423 AC: 2037 AN: 4814

European-Finnish (FIN) AF: 0.582 AC: 6136 AN: 10552

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35014 AN: 67948

Other (OTH) AF: 0.401 AC: 846 AN: 2112

Alfa AF: 0.469 Hom.: 10498

Bravo AF: 0.351

Asia WGS AF: 0.352 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11662668; hg19: chr18-20179381;