rs527790

Variant names:

• chr18-24480951-C-T
• rs527790

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 0.402 in 151,964 control chromosomes in the GnomAD database, including 13,097 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 0.40 (13097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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: 0.402 AC: 61056 AN: 151846 Hom.: 13080 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.00542

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.402 AC: 61109 AN: 151964 Hom.: 13097 Cov.: 32 AF XY: 0.391 AC XY: 29060 AN XY: 74246

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.00543

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.391

Alfa AF: 0.417 Hom.: 18194

Bravo AF: 0.398

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs527790; hg19: chr18-22060915;