ENST00000553776.1:n.569A>G

Variant names:

• chr14-68868725-T-C
• rs10151103
• ENST00000553776.1:n.569A>G

Variant summary

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

The ENST00000553776.1(BLZF2P):​n.569A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.713 in 540,356 control chromosomes in the GnomAD database, including 139,336 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 (36055 hom., cov: 30)
  • Exomes 𝑓: 0.72 (103281 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.28
• Publications: 2 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=-0.55).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLZF2P		n.68868725T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLZF2P	ENST00000553776.1	n.569A>G		non_coding_transcript_exon_variant	Exon 3 of 4	6

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104065 AN: 150852 Hom.: 36024 Cov.: 30

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.692

GnomAD4 exome AF: 0.722 AC: 280960 AN: 389386 Hom.: 103281 Cov.: 0 AF XY: 0.722 AC XY: 156543 AN XY: 216930

African (AFR) AF: 0.695 AC: 6728 AN: 9678

American (AMR) AF: 0.819 AC: 21705 AN: 26498

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 8394 AN: 11180

East Asian (EAS) AF: 0.518 AC: 9965 AN: 19234

South Asian (SAS) AF: 0.756 AC: 38314 AN: 50672

European-Finnish (FIN) AF: 0.692 AC: 20478 AN: 29574

Middle Eastern (MID) AF: 0.703 AC: 2094 AN: 2978

European-Non Finnish (NFE) AF: 0.723 AC: 158862 AN: 219736

Other (OTH) AF: 0.727 AC: 14420 AN: 19836

GnomAD4 genome AF: 0.690 AC: 104141 AN: 150970 Hom.: 36055 Cov.: 30 AF XY: 0.691 AC XY: 50855 AN XY: 73638

African (AFR) AF: 0.676 AC: 27794 AN: 41128

American (AMR) AF: 0.769 AC: 11667 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2509 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2546 AN: 5088

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

European-Finnish (FIN) AF: 0.665 AC: 6926 AN: 10410

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 46811 AN: 67632

Other (OTH) AF: 0.695 AC: 1459 AN: 2098

Alfa AF: 0.687 Hom.: 4520

Bravo AF: 0.695

Asia WGS AF: 0.702 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.2
DANN	Benign	0.63
PhyloP100		5.3

Splicing

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

Other links and lift over

dbSNP: rs10151103; hg19: chr14-69335442;