rs527790

Variant names:

• chr18-24480951-C-T
• rs527790

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 0.402 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.473 AC: 19573 AN: 41416

American (AMR) AF: 0.291 AC: 4444 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3470

East Asian (EAS) AF: 0.00543 AC: 28 AN: 5152

South Asian (SAS) AF: 0.232 AC: 1119 AN: 4814

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10554

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29280 AN: 67962

Other (OTH) AF: 0.391 AC: 826 AN: 2112

Alfa AF: 0.419 Hom.: 39913

Bravo AF: 0.398

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.71
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs527790; hg19: chr18-22060915;