1-169382828-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• 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 rank	MANE	Protein	UniProt
BLZF1	NM_001320973.2	c.1017+547C>T		intron_variant	Intron 6 of 6	ENST00000367808.8	NP_001307902.1
BLZF1	NM_003666.4	c.1017+547C>T		intron_variant	Intron 6 of 7		NP_003657.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLZF1	ENST00000367808.8	c.1017+547C>T		intron_variant	Intron 6 of 6	1	NM_001320973.2	ENSP00000356782.3
BLZF1	ENST00000329281.6	c.1017+547C>T		intron_variant	Intron 6 of 7	1		ENSP00000327541.2

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

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.0181

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0127 Hom.: 4

Bravo AF: 0.0783

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.56

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: rs1533518; hg19: chr1-169352066;