rs2032224

chr18-63509033-C-Achr18-63509033-C-Gchr18-63509033-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 0.57 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.570 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

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.617

Alfa AF: 0.667 Hom.: 45148

Bravo AF: 0.549

Asia WGS AF: 0.666 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.084
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032224; hg19: chr18-61176266;