rs2418453

Positions:

• chr18-30098322-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 0.275 in 152,002 control chromosomes in the GnomAD database, including 7,099 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 0.27 (7099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41802 AN: 151884 Hom.: 7096 Cov.: 32

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.275 AC: 41799 AN: 152002 Hom.: 7099 Cov.: 32 AF XY: 0.278 AC XY: 20632 AN XY: 74312

Gnomad4 AFR AF: 0.0879

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.256

Alfa AF: 0.347 Hom.: 5145

Bravo AF: 0.248

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2418453; hg19: chr18-27678287;