rs1517037

Positions:

• chr18-59211042-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.227

Alfa AF: 0.189 Hom.: 5157

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517037; hg19: chr18-56878274;