chr18-52244453-G-A

Variant names:

• chr18-52244453-G-A
• rs1445093

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 0.456 in 151,402 control chromosomes in the GnomAD database, including 16,307 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 (16307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69042 AN: 151284 Hom.: 16310 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.456 AC: 69052 AN: 151402 Hom.: 16307 Cov.: 31 AF XY: 0.452 AC XY: 33397 AN XY: 73952

African (AFR) AF: 0.349 AC: 14435 AN: 41372

American (AMR) AF: 0.326 AC: 4933 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1767 AN: 3458

East Asian (EAS) AF: 0.504 AC: 2577 AN: 5116

South Asian (SAS) AF: 0.484 AC: 2328 AN: 4814

European-Finnish (FIN) AF: 0.495 AC: 5184 AN: 10476

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36296 AN: 67714

Other (OTH) AF: 0.457 AC: 961 AN: 2104

Alfa AF: 0.512 Hom.: 85320

Bravo AF: 0.439

Asia WGS AF: 0.476 AC: 1643 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1445093; hg19: chr18-49770823;