chr14-68868125-G-C

Variant names:

• chr14-68868125-G-C
• rs1742886
• ENST00000553776.1:n.862C>G

Variant summary

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

The ENST00000553776.1(BLZF2P):​n.862C>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 0.71 in 1,270,538 control chromosomes in the GnomAD database, including 322,206 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 (36324 hom., cov: 31)
  • Exomes 𝑓: 0.71 (285882 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.88
• Publications: 11 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.759 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.862C>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104691 AN: 151642 Hom.: 36293 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.691

GnomAD4 exome AF: 0.713 AC: 797321 AN: 1118776 Hom.: 285882 Cov.: 17 AF XY: 0.712 AC XY: 406999 AN XY: 571414

African (AFR) AF: 0.690 AC: 18299 AN: 26532

American (AMR) AF: 0.808 AC: 34334 AN: 42474

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 16920 AN: 23370

East Asian (EAS) AF: 0.448 AC: 16766 AN: 37418

South Asian (SAS) AF: 0.754 AC: 59372 AN: 78744

European-Finnish (FIN) AF: 0.664 AC: 33810 AN: 50896

Middle Eastern (MID) AF: 0.707 AC: 3505 AN: 4960

European-Non Finnish (NFE) AF: 0.720 AC: 580477 AN: 806520

Other (OTH) AF: 0.707 AC: 33838 AN: 47862

GnomAD4 genome AF: 0.690 AC: 104767 AN: 151762 Hom.: 36324 Cov.: 31 AF XY: 0.691 AC XY: 51220 AN XY: 74146

African (AFR) AF: 0.676 AC: 27981 AN: 41366

American (AMR) AF: 0.771 AC: 11758 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2508 AN: 3462

East Asian (EAS) AF: 0.500 AC: 2569 AN: 5142

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

European-Finnish (FIN) AF: 0.664 AC: 6978 AN: 10512

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

European-Non Finnish (NFE) AF: 0.693 AC: 47056 AN: 67894

Other (OTH) AF: 0.695 AC: 1466 AN: 2110

Alfa AF: 0.590 Hom.: 1609

Bravo AF: 0.696

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.9
DANN	Benign	0.31
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs1742886; hg19: chr14-69334842;