14-54106263-A-G

Position:

• chr14-54106263-A-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 0.556 in 152,158 control chromosomes in the GnomAD database, including 26,025 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 0.56 (26025 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54106263A>G		intergenic_region
LOC105370507	XR_943882.3	n.665-14166T>C		intron_variant
LOC105370507	XR_943883.3	n.665-61132T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84598 AN: 152040 Hom.: 26025 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.556 AC: 84611 AN: 152158 Hom.: 26025 Cov.: 33 AF XY: 0.561 AC XY: 41724 AN XY: 74360

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.578

Alfa AF: 0.651 Hom.: 7755

Bravo AF: 0.526

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.43
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12432287; hg19: chr14-54572981;