rs17516734

Positions:

• chr1-169393965-G-A

Variant summary

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

The ENST00000329281.6(BLZF1):​c.*28-1929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,216 control chromosomes in the GnomAD database, including 187 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 0.043 (187 hom., cov: 31)
• Consequence: BLZF1 ENST00000329281.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

BLZF1 (HGNC:1065): (basic leucine zipper nuclear factor 1) Enables ubiquitin protein ligase binding activity. Acts upstream of or within Golgi organization and Golgi to plasma membrane protein transport. Located in Golgi apparatus and nucleoplasm. Biomarker of hepatocellular carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLZF1	NM_003666.4	c.*28-1929G>A		intron_variant			NP_003657.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLZF1	ENST00000329281.6	c.*28-1929G>A		intron_variant		1		ENSP00000327541	P1

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6586 AN: 152098 Hom.: 187 Cov.: 31

Gnomad AFR AF: 0.00966

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0549

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0473

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0433 AC: 6590 AN: 152216 Hom.: 187 Cov.: 31 AF XY: 0.0437 AC XY: 3255 AN XY: 74428

Gnomad4 AFR AF: 0.00963

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.0103

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0553

Gnomad4 OTH AF: 0.0496

Alfa AF: 0.0588 Hom.: 378

Bravo AF: 0.0408

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17516734; hg19: chr1-169363203;