18-50219296-T-C

Variant names:

• chr18-50219296-T-C
• rs1822466

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 0.457 in 151,970 control chromosomes in the GnomAD database, including 16,558 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 0.46 (16558 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• 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 (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.457 AC: 69461 AN: 151852 Hom.: 16544 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.457 AC: 69510 AN: 151970 Hom.: 16558 Cov.: 31 AF XY: 0.464 AC XY: 34458 AN XY: 74316

African (AFR) AF: 0.458 AC: 18952 AN: 41424

American (AMR) AF: 0.505 AC: 7721 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3464

East Asian (EAS) AF: 0.857 AC: 4413 AN: 5152

South Asian (SAS) AF: 0.486 AC: 2338 AN: 4808

European-Finnish (FIN) AF: 0.456 AC: 4820 AN: 10568

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28429 AN: 67958

Other (OTH) AF: 0.442 AC: 934 AN: 2112

Alfa AF: 0.349 Hom.: 1203

Bravo AF: 0.462

Asia WGS AF: 0.663 AC: 2302 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	1.3
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1822466; hg19: chr18-47745666;