rs17106421

Positions:

• chr14-68867839-C-G

Variant summary

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

The 14-68867839-C-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 381,058 control chromosomes in the GnomAD database, including 798 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 0.068 (393 hom., cov: 32)
  • Exomes 𝑓: 0.051 (405 hom.)
• Consequence: BLZF2P ENST00000553776.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 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			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10297 AN: 152084 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.0505 AC: 11559 AN: 228856 Hom.: 405 Cov.: 0 AF XY: 0.0475 AC XY: 5926 AN XY: 124784

Gnomad4 AFR exome AF: 0.0814

Gnomad4 AMR exome AF: 0.103

Gnomad4 ASJ exome AF: 0.0255

Gnomad4 EAS exome AF: 0.140

Gnomad4 SAS exome AF: 0.0151

Gnomad4 FIN exome AF: 0.0380

Gnomad4 NFE exome AF: 0.0471

Gnomad4 OTH exome AF: 0.0540

GnomAD4 genome AF: 0.0677 AC: 10300 AN: 152202 Hom.: 393 Cov.: 32 AF XY: 0.0670 AC XY: 4989 AN XY: 74422

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0155

Gnomad4 FIN AF: 0.0434

Gnomad4 NFE AF: 0.0520

Gnomad4 OTH AF: 0.0733

Alfa AF: 0.0575 Hom.: 36

Bravo AF: 0.0761

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.0
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: rs17106421; hg19: chr14-69334556;