rs10139069

Positions:

• chr14-68868721-G-A
• chr14-68868721-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553776.1(BLZF2P):​n.573C>T 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 0.702 in 529,442 control chromosomes in the GnomAD database, including 132,740 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 0.66 (33233 hom., cov: 29)
  • Exomes 𝑓: 0.72 (99507 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLZF2P	ENST00000553776.1	n.573C>T		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.661 AC: 99574 AN: 150752 Hom.: 33202 Cov.: 29

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.672

GnomAD4 exome AF: 0.719 AC: 272259 AN: 378574 Hom.: 99507 Cov.: 0 AF XY: 0.719 AC XY: 151843 AN XY: 211218

Gnomad4 AFR exome AF: 0.603

Gnomad4 AMR exome AF: 0.818

Gnomad4 ASJ exome AF: 0.753

Gnomad4 EAS exome AF: 0.524

Gnomad4 SAS exome AF: 0.745

Gnomad4 FIN exome AF: 0.693

Gnomad4 NFE exome AF: 0.725

Gnomad4 OTH exome AF: 0.722

GnomAD4 genome AF: 0.661 AC: 99652 AN: 150868 Hom.: 33233 Cov.: 29 AF XY: 0.661 AC XY: 48666 AN XY: 73584

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.676

Alfa AF: 0.665 Hom.: 3872

Bravo AF: 0.661

Asia WGS AF: 0.683 AC: 2372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10139069; hg19: chr14-69335438;