rs502933

Variant names:

• chr18-60229241-C-A
• rs502933

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 0.376 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.519 AC: 21517 AN: 41436

American (AMR) AF: 0.250 AC: 3824 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1010 AN: 5174

South Asian (SAS) AF: 0.474 AC: 2281 AN: 4814

European-Finnish (FIN) AF: 0.327 AC: 3450 AN: 10564

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22865 AN: 67938

Other (OTH) AF: 0.340 AC: 719 AN: 2112

Alfa AF: 0.386 Hom.: 4230

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs502933; hg19: chr18-57896474;