14-54453705-T-G

Position:

• chr14-54453705-T-G

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 0.2 in 151,854 control chromosomes in the GnomAD database, including 3,581 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 0.20 (3581 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54453705T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30237 AN: 151738 Hom.: 3572 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0867

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0895

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.200 AC: 30301 AN: 151854 Hom.: 3581 Cov.: 32 AF XY: 0.195 AC XY: 14483 AN XY: 74200

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0895

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.162

Alfa AF: 0.158 Hom.: 4259

Bravo AF: 0.207

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11850320; hg19: chr14-54920423;