rs1991923

chr11-85658154-C-T

Variant summary

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

The NM_001039618.4(CREBZF):c.*5657G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,776 control chromosomes in the GnomAD database, including 1,462 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 0.13 (1462 hom., cov: 33)
• Consequence: CREBZF NM_001039618.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

CREBZF (HGNC:24905): (CREB/ATF bZIP transcription factor) Enables identical protein binding activity. Involved in negative regulation of gene expression, epigenetic; regulation of transcription, DNA-templated; and response to virus. Located in mitochondrion and nucleoplasm. [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 = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CREBZF	NM_001039618.4	c.*5657G>A		3_prime_UTR_variant	1/1	ENST00000527447.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CREBZF	ENST00000527447.2	c.*5657G>A		3_prime_UTR_variant	1/1		NM_001039618.4	P1
CREBZF	ENST00000682836.1	c.*2690G>A		3_prime_UTR_variant, NMD_transcript_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19035 AN: 151660 Hom.: 1451 Cov.: 33

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.126 AC: 19062 AN: 151776 Hom.: 1462 Cov.: 33 AF XY: 0.132 AC XY: 9805 AN XY: 74196

Gnomad4 AFR AF: 0.0891

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.136

Alfa AF: 0.122 Hom.: 1162

Bravo AF: 0.130

Asia WGS AF: 0.288 AC: 996 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.92
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991923; hg19: chr11-85369198;