14-68868125-G-C

Position:

• chr14-68868125-G-C

Variant summary

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

The ENST00000553776.1(BLZF2P):​n.862C>G 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 0.71 in 1,270,538 control chromosomes in the GnomAD database, including 322,206 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 (36324 hom., cov: 31)
  • Exomes 𝑓: 0.71 (285882 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.88

Genes affected

BLZF2P (HGNC:):

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 = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLZF2P		n.68868125G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLZF2P	ENST00000553776.1	n.862C>G		non_coding_transcript_exon_variant	4/4	6

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104691 AN: 151642 Hom.: 36293 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.724

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: 0.691

GnomAD4 exome AF: 0.713 AC: 797321 AN: 1118776 Hom.: 285882 Cov.: 17 AF XY: 0.712 AC XY: 406999 AN XY: 571414

Gnomad4 AFR exome AF: 0.690

Gnomad4 AMR exome AF: 0.808

Gnomad4 ASJ exome AF: 0.724

Gnomad4 EAS exome AF: 0.448

Gnomad4 SAS exome AF: 0.754

Gnomad4 FIN exome AF: 0.664

Gnomad4 NFE exome AF: 0.720

Gnomad4 OTH exome AF: 0.707

GnomAD4 genome AF: 0.690 AC: 104767 AN: 151762 Hom.: 36324 Cov.: 31 AF XY: 0.691 AC XY: 51220 AN XY: 74146

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.695

Alfa AF: 0.590 Hom.: 1609

Bravo AF: 0.696

Asia WGS AF: 0.703 AC: 2443 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	6.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1742886; hg19: chr14-69334842;