18-30265212-A-C

Variant names:

• chr18-30265212-A-C
• rs9304554

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 0.192 in 151,340 control chromosomes in the GnomAD database, including 3,106 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 0.19 (3106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.193 AC: 29126 AN: 151222 Hom.: 3102 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.192 AC: 29130 AN: 151340 Hom.: 3106 Cov.: 32 AF XY: 0.194 AC XY: 14380 AN XY: 73948

African (AFR) AF: 0.116 AC: 4790 AN: 41470

American (AMR) AF: 0.138 AC: 2091 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 693 AN: 3450

East Asian (EAS) AF: 0.169 AC: 867 AN: 5138

South Asian (SAS) AF: 0.195 AC: 938 AN: 4822

European-Finnish (FIN) AF: 0.303 AC: 3202 AN: 10552

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 15949 AN: 67446

Other (OTH) AF: 0.186 AC: 390 AN: 2100

Alfa AF: 0.123 Hom.: 259

Bravo AF: 0.173

Asia WGS AF: 0.144 AC: 501 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.69
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs9304554; hg19: chr18-27845177;