chr18-30277820-A-G

Position:

• chr18-30277820-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 0.234 in 150,444 control chromosomes in the GnomAD database, including 4,692 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 0.23 (4692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 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: 0.234 AC: 35167 AN: 150326 Hom.: 4685 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.234 AC: 35176 AN: 150444 Hom.: 4692 Cov.: 31 AF XY: 0.228 AC XY: 16775 AN XY: 73486

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.246

Alfa AF: 0.282 Hom.: 2993

Bravo AF: 0.233

Asia WGS AF: 0.245 AC: 852 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2949535; hg19: chr18-27857785;