rs1599238

Variant names:

• chr18-57524381-C-G
• rs1599238

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 0.328 in 152,100 control chromosomes in the GnomAD database, including 10,155 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 0.33 (10155 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 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: 0.329 AC: 49975 AN: 151982 Hom.: 10153 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.328 AC: 49964 AN: 152100 Hom.: 10155 Cov.: 33 AF XY: 0.321 AC XY: 23845 AN XY: 74314

African (AFR) AF: 0.107 AC: 4432 AN: 41508

American (AMR) AF: 0.302 AC: 4619 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1309 AN: 3468

East Asian (EAS) AF: 0.156 AC: 810 AN: 5178

South Asian (SAS) AF: 0.244 AC: 1174 AN: 4820

European-Finnish (FIN) AF: 0.414 AC: 4362 AN: 10542

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32007 AN: 67980

Other (OTH) AF: 0.338 AC: 714 AN: 2114

Alfa AF: 0.397 Hom.: 1659

Bravo AF: 0.310

Asia WGS AF: 0.227 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1599238; hg19: chr18-55191613;