rs9304456

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;