18-59211042-C-T

Variant names:

• chr18-59211042-C-T
• rs1517037

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 0.232 in 152,070 control chromosomes in the GnomAD database, including 4,390 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 0.23 (4390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 24 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 (AFR) allele frequency at 95% confidence interval = 0.294 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: 0.232 AC: 35243 AN: 151952 Hom.: 4375 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.232 AC: 35299 AN: 152070 Hom.: 4390 Cov.: 33 AF XY: 0.237 AC XY: 17608 AN XY: 74340

African (AFR) AF: 0.298 AC: 12369 AN: 41454

American (AMR) AF: 0.239 AC: 3657 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3472

East Asian (EAS) AF: 0.189 AC: 982 AN: 5188

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4818

European-Finnish (FIN) AF: 0.292 AC: 3086 AN: 10566

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12494 AN: 67972

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.196 Hom.: 12279

Bravo AF: 0.235

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.50
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs1517037; hg19: chr18-56878274;