chr14-55926388-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000259868 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612704.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259868	ENST00000612704.1	TSL:5	n.44-17252A>G		intron	N/A
	ENSG00000259868	ENST00000664335.2		n.150-17252A>G		intron	N/A
	ENSG00000259868	ENST00000729158.1		n.585-17252A>G		intron	N/A

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

African (AFR) AF: 0.721 AC: 29845 AN: 41394

American (AMR) AF: 0.272 AC: 4161 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3470

East Asian (EAS) AF: 0.106 AC: 544 AN: 5156

South Asian (SAS) AF: 0.282 AC: 1363 AN: 4826

European-Finnish (FIN) AF: 0.187 AC: 1975 AN: 10570

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11100 AN: 67958

Other (OTH) AF: 0.297 AC: 626 AN: 2108

Alfa AF: 0.211 Hom.: 9121

Bravo AF: 0.354

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.093
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4898878; hg19: chr14-56393106;