rs4293296

Variant names:

• chr14-54390568-G-A
• rs4293296

Your query was ambiguous. Multiple possible variants found:

• chr14-54390568-G-A
• chr14-54390568-G-T

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 0.258 in 150,164 control chromosomes in the GnomAD database, including 5,152 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 0.26 (5152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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: 0.258 AC: 38723 AN: 150046 Hom.: 5144 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.258 AC: 38758 AN: 150164 Hom.: 5152 Cov.: 32 AF XY: 0.254 AC XY: 18577 AN XY: 73160

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.232

Alfa AF: 0.262 Hom.: 8472

Bravo AF: 0.263

Asia WGS AF: 0.165 AC: 573 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4293296; hg19: chr14-54857286;