chr18-63509033-C-A

Variant names:

• chr18-63509033-C-A
• rs2032224

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 0.57 in 152,138 control chromosomes in the GnomAD database, including 27,286 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 0.57 (27286 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86680 AN: 152018 Hom.: 27279 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.570 AC: 86707 AN: 152138 Hom.: 27286 Cov.: 33 AF XY: 0.576 AC XY: 42807 AN XY: 74366

African (AFR) AF: 0.284 AC: 11784 AN: 41476

American (AMR) AF: 0.611 AC: 9343 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3472

East Asian (EAS) AF: 0.804 AC: 4160 AN: 5174

South Asian (SAS) AF: 0.579 AC: 2793 AN: 4824

European-Finnish (FIN) AF: 0.720 AC: 7626 AN: 10590

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46386 AN: 67994

Other (OTH) AF: 0.617 AC: 1303 AN: 2112

Alfa AF: 0.652 Hom.: 60990

Bravo AF: 0.549

Asia WGS AF: 0.666 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.084
DANN	Benign	0.60
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs2032224; hg19: chr18-61176266;