rs10494478

chr1-169372489-A-G

Variant summary

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

The NM_001320973.2(BLZF1):c.28+2939A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,224 control chromosomes in the GnomAD database, including 729 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 0.084 (729 hom., cov: 32)
• Consequence: BLZF1 NM_001320973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLZF1	NM_001320973.2	c.28+2939A>G		intron_variant		ENST00000367808.8
BLZF1	NM_001320972.2	c.28+2939A>G		intron_variant
BLZF1	NM_003666.4	c.28+2939A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLZF1	ENST00000367808.8	c.28+2939A>G		intron_variant		1	NM_001320973.2	P1

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12822 AN: 152106 Hom.: 729 Cov.: 32

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0842 AC: 12818 AN: 152224 Hom.: 729 Cov.: 32 AF XY: 0.0873 AC XY: 6500 AN XY: 74428

Gnomad4 AFR AF: 0.0192

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0247

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0953 Hom.: 108

Bravo AF: 0.0868

Asia WGS AF: 0.0580 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.39

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: rs10494478; hg19: chr1-169341727;