1-169382828-C-T

Variant names:

• chr1-169382828-C-T
• rs1533518
• NM_001320973.2:c.1017+547C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001320973.2(BLZF1):​c.1017+547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0746 in 152,204 control chromosomes in the GnomAD database, including 1,541 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 0.075 (1541 hom., cov: 32)
• Consequence: BLZF1 NM_001320973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320973.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF1	NM_001320973.2	MANE Select	c.1017+547C>T		intron	N/A	NP_001307902.1	Q9H2G9-1
	BLZF1	NM_003666.4		c.1017+547C>T		intron	N/A	NP_003657.1	Q9H2G9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF1	ENST00000367808.8	TSL:1 MANE Select	c.1017+547C>T		intron	N/A	ENSP00000356782.3	Q9H2G9-1
	BLZF1	ENST00000329281.6	TSL:1	c.1017+547C>T		intron	N/A	ENSP00000327541.2	Q9H2G9-1
	BLZF1	ENST00000899417.1		c.1068+547C>T		intron	N/A	ENSP00000569476.1

Frequencies

GnomAD3 genomes AF: 0.0745 AC: 11333 AN: 152086 Hom.: 1536 Cov.: 32

Gnomad AFR AF: 0.0795

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0746 AC: 11358 AN: 152204 Hom.: 1541 Cov.: 32 AF XY: 0.0824 AC XY: 6131 AN XY: 74410

African (AFR) AF: 0.0797 AC: 3310 AN: 41534

American (AMR) AF: 0.0930 AC: 1422 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0426 AC: 148 AN: 3472

East Asian (EAS) AF: 0.665 AC: 3428 AN: 5156

South Asian (SAS) AF: 0.149 AC: 716 AN: 4820

European-Finnish (FIN) AF: 0.0859 AC: 910 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1233 AN: 68022

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0164 Hom.: 12

Bravo AF: 0.0783

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1533518; hg19: chr1-169352066;