rs9304456

Variant names:

• chr18-53994250-G-A
• rs9304456

Your query was ambiguous. Multiple possible variants found:

• chr18-53994250-G-A
• chr18-53994250-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.207 in 152,084 control chromosomes in the GnomAD database, including 3,433 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 0.21 (3433 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.207 AC: 31436 AN: 151966 Hom.: 3429 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.207 AC: 31446 AN: 152084 Hom.: 3433 Cov.: 33 AF XY: 0.204 AC XY: 15176 AN XY: 74344

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.189

Alfa AF: 0.217 Hom.: 1924

Bravo AF: 0.201

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9304456; hg19: chr18-51520620;