ENST00000329281.6:c.*28-1929G>A

Variant names:

• chr1-169393965-G-A
• rs17516734
• ENST00000329281.6:c.*28-1929G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000329281.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF1	NM_003666.4		c.*28-1929G>A		intron	N/A	NP_003657.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF1	ENST00000329281.6	TSL:1	c.*28-1929G>A		intron	N/A	ENSP00000327541.2

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

African (AFR) AF: 0.00963 AC: 400 AN: 41550

American (AMR) AF: 0.0547 AC: 836 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.0103 AC: 53 AN: 5160

South Asian (SAS) AF: 0.103 AC: 496 AN: 4824

European-Finnish (FIN) AF: 0.0475 AC: 504 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3761 AN: 67994

Other (OTH) AF: 0.0496 AC: 105 AN: 2116

Alfa AF: 0.0565 Hom.: 463

Bravo AF: 0.0408

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.6
DANN	Benign	0.85
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17516734; hg19: chr1-169363203;