rs502933

Positions:

• chr18-60229241-C-A

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 0.376 in 152,002 control chromosomes in the GnomAD database, including 11,540 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 (11540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57080 AN: 151884 Hom.: 11511 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.376 AC: 57149 AN: 152002 Hom.: 11540 Cov.: 32 AF XY: 0.373 AC XY: 27746 AN XY: 74318

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.340

Alfa AF: 0.339 Hom.: 2057

Bravo AF: 0.374

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.016
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs502933; hg19: chr18-57896474;