ENST00000553776.1:n.588C>T

Variant names:

• chr14-68868706-G-A
• rs10139065
• ENST00000553776.1:n.588C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553776.1(BLZF2P):​n.588C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.706 in 439,280 control chromosomes in the GnomAD database, including 110,805 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 0.69 (36051 hom., cov: 29)
  • Exomes 𝑓: 0.71 (74754 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.45
• Publications: 5 publications found

Genes affected

BLZF2P (HGNC:20049): (basic leucine zipper nuclear factor 2, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553776.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF2P	ENST00000553776.1	TSL:6	n.588C>T		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104004 AN: 150626 Hom.: 36020 Cov.: 29

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.690

GnomAD4 exome AF: 0.714 AC: 206001 AN: 288536 Hom.: 74754 Cov.: 0 AF XY: 0.713 AC XY: 115165 AN XY: 161492

African (AFR) AF: 0.688 AC: 4465 AN: 6486

American (AMR) AF: 0.815 AC: 15536 AN: 19056

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 5742 AN: 7668

East Asian (EAS) AF: 0.508 AC: 7102 AN: 13968

South Asian (SAS) AF: 0.745 AC: 26332 AN: 35334

European-Finnish (FIN) AF: 0.684 AC: 15640 AN: 22850

Middle Eastern (MID) AF: 0.701 AC: 1828 AN: 2606

European-Non Finnish (NFE) AF: 0.716 AC: 118766 AN: 165808

Other (OTH) AF: 0.717 AC: 10590 AN: 14760

GnomAD4 genome AF: 0.690 AC: 104080 AN: 150744 Hom.: 36051 Cov.: 29 AF XY: 0.691 AC XY: 50808 AN XY: 73482

African (AFR) AF: 0.676 AC: 27770 AN: 41056

American (AMR) AF: 0.769 AC: 11650 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2535 AN: 5060

South Asian (SAS) AF: 0.750 AC: 3606 AN: 4806

European-Finnish (FIN) AF: 0.670 AC: 6895 AN: 10288

Middle Eastern (MID) AF: 0.669 AC: 194 AN: 290

European-Non Finnish (NFE) AF: 0.692 AC: 46823 AN: 67638

Other (OTH) AF: 0.694 AC: 1462 AN: 2106

Alfa AF: 0.697 Hom.: 48951

Bravo AF: 0.695

Asia WGS AF: 0.701 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.2
DANN	Benign	0.50
PhyloP100		4.5

Splicing

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

Other links and lift over

dbSNP: rs10139065; hg19: chr14-69335423;