rs9304221

chr18-40422697-T-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;