chr18-30516558-A-G

Position:

• chr18-30516558-A-G

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 0.352 in 152,084 control chromosomes in the GnomAD database, including 9,706 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 0.35 (9706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.352 AC: 53469 AN: 151970 Hom.: 9693 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.352 AC: 53515 AN: 152084 Hom.: 9706 Cov.: 32 AF XY: 0.347 AC XY: 25782 AN XY: 74338

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.321

Alfa AF: 0.380 Hom.: 1378

Bravo AF: 0.339

Asia WGS AF: 0.235 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9304560; hg19: chr18-28096524;