14-68868145-G-A

Variant names:

• chr14-68868145-G-A
• rs1742498
• ENST00000553776.1:n.842C>T

Variant summary

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

The ENST00000553776.1(BLZF2P):​n.842C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.712 in 1,170,736 control chromosomes in the GnomAD database, including 299,374 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 (36342 hom., cov: 32)
  • Exomes 𝑓: 0.72 (263032 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.77
• 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=-0.51).
• 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF2P	ENST00000553776.1	TSL:6	n.842C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104732 AN: 151688 Hom.: 36311 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.725

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: 0.692

GnomAD4 exome AF: 0.716 AC: 729250 AN: 1018928 Hom.: 263032 Cov.: 14 AF XY: 0.715 AC XY: 376062 AN XY: 526016

African (AFR) AF: 0.691 AC: 17026 AN: 24628

American (AMR) AF: 0.808 AC: 34529 AN: 42724

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 16457 AN: 22712

East Asian (EAS) AF: 0.447 AC: 16502 AN: 36916

South Asian (SAS) AF: 0.755 AC: 58299 AN: 77246

European-Finnish (FIN) AF: 0.664 AC: 33815 AN: 50934

Middle Eastern (MID) AF: 0.706 AC: 3371 AN: 4774

European-Non Finnish (NFE) AF: 0.725 AC: 517626 AN: 714378

Other (OTH) AF: 0.709 AC: 31625 AN: 44616

GnomAD4 genome AF: 0.690 AC: 104808 AN: 151808 Hom.: 36342 Cov.: 32 AF XY: 0.691 AC XY: 51242 AN XY: 74178

African (AFR) AF: 0.677 AC: 27989 AN: 41370

American (AMR) AF: 0.771 AC: 11760 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2509 AN: 3462

East Asian (EAS) AF: 0.500 AC: 2575 AN: 5152

South Asian (SAS) AF: 0.750 AC: 3606 AN: 4810

European-Finnish (FIN) AF: 0.664 AC: 6981 AN: 10520

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

European-Non Finnish (NFE) AF: 0.693 AC: 47076 AN: 67922

Other (OTH) AF: 0.695 AC: 1467 AN: 2110

Alfa AF: 0.693 Hom.: 13132

Bravo AF: 0.696

Asia WGS AF: 0.704 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.64
PhyloP100		6.8

Splicing

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

Other links and lift over

dbSNP: rs1742498; hg19: chr14-69334862;