rs527790

chr18-24480951-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 0.402 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;