rs10151103

Positions:

• chr14-68868725-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.55).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLZF2P	ENST00000553776.1	n.569A>G		non_coding_transcript_exon_variant	3/4

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

Gnomad4 AFR exome AF: 0.695

Gnomad4 AMR exome AF: 0.819

Gnomad4 ASJ exome AF: 0.751

Gnomad4 EAS exome AF: 0.518

Gnomad4 SAS exome AF: 0.756

Gnomad4 FIN exome AF: 0.692

Gnomad4 NFE exome AF: 0.723

Gnomad4 OTH exome AF: 0.727

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

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.695

Alfa AF: 0.687 Hom.: 4345

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10151103; hg19: chr14-69335442;