chr14-51290118-A-G

Position:

• chr14-51290118-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 0.0369 in 152,282 control chromosomes in the GnomAD database, including 116 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 0.037 (116 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.51290118A>G		intergenic_region
LOC124903315	XR_007064164.1	n.633+2055A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0368 AC: 5599 AN: 152164 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0761

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0369

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0369 AC: 5612 AN: 152282 Hom.: 116 Cov.: 32 AF XY: 0.0380 AC XY: 2831 AN XY: 74464

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.0763

Gnomad4 SAS AF: 0.0630

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.0369

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0384 Hom.: 18

Bravo AF: 0.0344

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4078416; hg19: chr14-51756836;