rs1806584
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000353267.8(CREB1):c.*4488A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 199,054 control chromosomes in the GnomAD database, including 2,253 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 ( 1646 hom., cov: 32)
Exomes 𝑓: 0.14 ( 607 hom. )
Consequence
CREB1
ENST00000353267.8 3_prime_UTR
ENST00000353267.8 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.237
Genes affected
CREB1 (HGNC:2345): (cAMP responsive element binding protein 1) This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in several transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]
METTL21A (HGNC:30476): (methyltransferase 21A, HSPA lysine) Enables ATPase binding activity; Hsp70 protein binding activity; and protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CREB1 | NM_004379.5 | c.*4488A>G | 3_prime_UTR_variant | 8/8 | ENST00000353267.8 | NP_004370.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CREB1 | ENST00000353267.8 | c.*4488A>G | 3_prime_UTR_variant | 8/8 | 1 | NM_004379.5 | ENSP00000236995 | P1 |
Frequencies
GnomAD3 genomes AF: 0.127 AC: 19377AN: 152106Hom.: 1646 Cov.: 32
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GnomAD4 exome AF: 0.140 AC: 6577AN: 46830Hom.: 607 Cov.: 0 AF XY: 0.142 AC XY: 3104AN XY: 21794
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GnomAD4 genome AF: 0.127 AC: 19371AN: 152224Hom.: 1646 Cov.: 32 AF XY: 0.124 AC XY: 9194AN XY: 74428
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at