chr18-24482852-G-C

Variant names:

• chr18-24482852-G-C
• rs487202

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 0.346 in 151,896 control chromosomes in the GnomAD database, including 9,882 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 0.35 (9882 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 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: 0.346 AC: 52534 AN: 151778 Hom.: 9883 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.00521

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.346 AC: 52527 AN: 151896 Hom.: 9882 Cov.: 31 AF XY: 0.337 AC XY: 25027 AN XY: 74238

African (AFR) AF: 0.278 AC: 11492 AN: 41408

American (AMR) AF: 0.271 AC: 4134 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3468

East Asian (EAS) AF: 0.00522 AC: 27 AN: 5168

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3901 AN: 10498

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29227 AN: 67962

Other (OTH) AF: 0.354 AC: 745 AN: 2106

Alfa AF: 0.241 Hom.: 554

Bravo AF: 0.334

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.46
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs487202; hg19: chr18-22062816;