rs1533519

chr1-169382754-G-A

Variant summary

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

The NM_001320973.2(BLZF1):c.1017+473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0559 in 152,186 control chromosomes in the GnomAD database, including 1,391 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 0.056 (1391 hom., cov: 32)
• Consequence: BLZF1 NM_001320973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLZF1	NM_001320973.2	c.1017+473G>A		intron_variant		ENST00000367808.8
BLZF1	NM_003666.4	c.1017+473G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLZF1	ENST00000367808.8	c.1017+473G>A		intron_variant		1	NM_001320973.2	P1
BLZF1	ENST00000329281.6	c.1017+473G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8498 AN: 152068 Hom.: 1387 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0559 AC: 8513 AN: 152186 Hom.: 1391 Cov.: 32 AF XY: 0.0648 AC XY: 4821 AN XY: 74402

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0866

Gnomad4 NFE AF: 0.0166

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0344 Hom.: 39

Bravo AF: 0.0574

Asia WGS AF: 0.363 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.93
Dann	Benign	0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533519; hg19: chr1-169351992;