14-55926388-A-G

Variant names:

• chr14-55926388-A-G
• rs4898878
• ENST00000612704.1:n.44-17252A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612704.1(ENSG00000259868):​n.44-17252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,960 control chromosomes in the GnomAD database, including 12,990 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 0.33 (12990 hom., cov: 32)
• Consequence: ENSG00000259868 ENST00000612704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

ENSG00000259868 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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
ENSG00000259868	ENST00000612704.1	n.44-17252A>G		intron_variant	Intron 1 of 6	5
ENSG00000259868	ENST00000664335.1	n.148-17252A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50373 AN: 151842 Hom.: 12942 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.332 AC: 50487 AN: 151960 Hom.: 12990 Cov.: 32 AF XY: 0.330 AC XY: 24507 AN XY: 74276

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.297

Alfa AF: 0.188 Hom.: 4696

Bravo AF: 0.354

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.093
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4898878; hg19: chr14-56393106;