ENST00000553776.1:n.447A>G

Variant names:

• chr14-68868847-T-C
• rs7401911
• ENST00000553776.1:n.447A>G

Variant summary

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

The ENST00000553776.1(BLZF2P):​n.447A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 640,220 control chromosomes in the GnomAD database, including 163,781 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 (36304 hom., cov: 29)
  • Exomes 𝑓: 0.72 (127477 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67
• Publications: 4 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=-0.65).
• 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF2P	ENST00000553776.1	TSL:6	n.447A>G		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104557 AN: 151392 Hom.: 36273 Cov.: 29

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.692

GnomAD4 exome AF: 0.719 AC: 351184 AN: 488710 Hom.: 127477 Cov.: 0 AF XY: 0.719 AC XY: 194458 AN XY: 270336

African (AFR) AF: 0.696 AC: 8975 AN: 12904

American (AMR) AF: 0.815 AC: 29058 AN: 35644

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 11954 AN: 16094

East Asian (EAS) AF: 0.516 AC: 12074 AN: 23420

South Asian (SAS) AF: 0.754 AC: 48950 AN: 64948

European-Finnish (FIN) AF: 0.691 AC: 27331 AN: 39566

Middle Eastern (MID) AF: 0.704 AC: 2388 AN: 3392

European-Non Finnish (NFE) AF: 0.719 AC: 192725 AN: 268122

Other (OTH) AF: 0.720 AC: 17729 AN: 24620

GnomAD4 genome AF: 0.691 AC: 104632 AN: 151510 Hom.: 36304 Cov.: 29 AF XY: 0.691 AC XY: 51150 AN XY: 73990

African (AFR) AF: 0.677 AC: 27906 AN: 41250

American (AMR) AF: 0.770 AC: 11724 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2513 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2586 AN: 5148

South Asian (SAS) AF: 0.749 AC: 3607 AN: 4814

European-Finnish (FIN) AF: 0.665 AC: 6891 AN: 10362

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47093 AN: 67928

Other (OTH) AF: 0.696 AC: 1466 AN: 2106

Alfa AF: 0.692 Hom.: 147444

Bravo AF: 0.695

Asia WGS AF: 0.703 AC: 2442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.6
DANN	Benign	0.55
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs7401911; hg19: chr14-69335564;