rs10139065

chr14-68868706-G-Achr14-68868706-G-T

Variant summary

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

The ENST00000553776.1(BLZF2P):n.588C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.706 in 439,280 control chromosomes in the GnomAD database, including 110,805 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 (36051 hom., cov: 29)
  • Exomes 𝑓: 0.71 (74754 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.45

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=-0.64).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLZF2P	ENST00000553776.1	n.588C>T		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104004 AN: 150626 Hom.: 36020 Cov.: 29

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.690

GnomAD4 exome AF: 0.714 AC: 206001 AN: 288536 Hom.: 74754 Cov.: 0 AF XY: 0.713 AC XY: 115165 AN XY: 161492

Gnomad4 AFR exome AF: 0.688

Gnomad4 AMR exome AF: 0.815

Gnomad4 ASJ exome AF: 0.749

Gnomad4 EAS exome AF: 0.508

Gnomad4 SAS exome AF: 0.745

Gnomad4 FIN exome AF: 0.684

Gnomad4 NFE exome AF: 0.716

Gnomad4 OTH exome AF: 0.717

GnomAD4 genome AF: 0.690 AC: 104080 AN: 150744 Hom.: 36051 Cov.: 29 AF XY: 0.691 AC XY: 50808 AN XY: 73482

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.694

Alfa AF: 0.697 Hom.: 36883

Bravo AF: 0.695

Asia WGS AF: 0.701 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	9.2
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10139065; hg19: chr14-69335423;