14-68869414-T-C

Position:

• chr14-68869414-T-C

Variant summary

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

The variant allele was found at a frequency of 0.701 in 149,262 control chromosomes in the GnomAD database, including 36,407 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 0.70 (36231 hom., cov: 28)
  • Exomes 𝑓: 0.78 (176 hom.)
• Consequence: BLZF2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

Genes affected

BLZF2P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLZF2P		n.68869414T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLZF2P	ENST00000553776.1	n.223-51A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.701 AC: 104206 AN: 148602 Hom.: 36202 Cov.: 28

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.706

GnomAD4 exome AF: 0.780 AC: 426 AN: 546 Hom.: 176 AF XY: 0.772 AC XY: 247 AN XY: 320

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.833

Gnomad4 ASJ exome AF: 0.929

Gnomad4 EAS exome AF: 0.450

Gnomad4 SAS exome AF: 0.911

Gnomad4 FIN exome AF: 0.688

Gnomad4 NFE exome AF: 0.765

Gnomad4 OTH exome AF: 0.867

GnomAD4 genome AF: 0.701 AC: 104277 AN: 148716 Hom.: 36231 Cov.: 28 AF XY: 0.704 AC XY: 50937 AN XY: 72332

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.709

Alfa AF: 0.687 Hom.: 4366

Bravo AF: 0.695

Asia WGS AF: 0.701 AC: 2414 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	6.5
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902660; hg19: chr14-69336131;