rs9304221

Variant names:

• chr18-40422697-T-A
• rs9304221

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 0.222 in 152,080 control chromosomes in the GnomAD database, including 4,472 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 0.22 (4472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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: 0.222 AC: 33793 AN: 151962 Hom.: 4454 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.222 AC: 33836 AN: 152080 Hom.: 4472 Cov.: 32 AF XY: 0.230 AC XY: 17086 AN XY: 74330

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.216

Alfa AF: 0.210 Hom.: 467

Bravo AF: 0.228

Asia WGS AF: 0.520 AC: 1801 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9304221; hg19: chr18-38002661;