rs350852
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032607.3(CREB3L3):c.822-139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 819,526 control chromosomes in the GnomAD database, including 314,080 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.88 ( 59958 hom., cov: 32)
Exomes 𝑓: 0.87 ( 254122 hom. )
Consequence
CREB3L3
NM_032607.3 intron
NM_032607.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.743
Genes affected
CREB3L3 (HGNC:18855): (cAMP responsive element binding protein 3 like 3) This gene encodes a member of the basic-leucine zipper family and the AMP-dependent transcription factor family. The encoded protein is localized to the endoplasmic reticulum and acts as a transcription factor activated by cyclic AMP stimulation. The encoded protein binds the cyclic AMP response element (CRE) and the box-B element and has been linked to acute inflammatory response, hepatocellular carcinoma, triglyceride metabolism, and hepcidin expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 19-4170001-G-A is Benign according to our data. Variant chr19-4170001-G-A is described in ClinVar as [Benign]. Clinvar id is 1239450.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CREB3L3 | NM_032607.3 | c.822-139G>A | intron_variant | ENST00000078445.7 | |||
CREB3L3 | NM_001271995.2 | c.819-139G>A | intron_variant | ||||
CREB3L3 | NM_001271996.2 | c.816-139G>A | intron_variant | ||||
CREB3L3 | NM_001271997.2 | c.715-139G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CREB3L3 | ENST00000078445.7 | c.822-139G>A | intron_variant | 1 | NM_032607.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.885 AC: 134509AN: 152068Hom.: 59900 Cov.: 32
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GnomAD4 exome AF: 0.870 AC: 580918AN: 667340Hom.: 254122 AF XY: 0.875 AC XY: 312837AN XY: 357416
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GnomAD4 genome ? AF: 0.885 AC: 134627AN: 152186Hom.: 59958 Cov.: 32 AF XY: 0.879 AC XY: 65408AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at