rs10038
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015321.3(CRTC1):c.*4536C>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 0.274 in 230,316 control chromosomes in the GnomAD database, including 9,345 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 0.28 ( 6426 hom., cov: 33)
Exomes 𝑓: 0.26 ( 2919 hom. )
Consequence
CRTC1
NM_015321.3 3_prime_UTR
NM_015321.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.376
Genes affected
CRTC1 (HGNC:16062): (CREB regulated transcription coactivator 1) Enables cAMP response element binding protein binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol; nuclear body; and plasma membrane. [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=-0.77).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTC1 | NM_015321.3 | c.*4536C>A | 3_prime_UTR_variant | 14/14 | ENST00000321949.13 | ||
CRTC1 | NM_001098482.2 | c.*4536C>A | 3_prime_UTR_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTC1 | ENST00000321949.13 | c.*4536C>A | 3_prime_UTR_variant | 14/14 | 1 | NM_015321.3 | A1 | ||
CRTC1 | ENST00000338797.10 | c.*4536C>A | 3_prime_UTR_variant | 15/15 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.282 AC: 42943AN: 152044Hom.: 6428 Cov.: 33
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GnomAD4 exome AF: 0.259 AC: 20238AN: 78154Hom.: 2919 Cov.: 0 AF XY: 0.257 AC XY: 9259AN XY: 36000
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GnomAD4 genome ? AF: 0.282 AC: 42943AN: 152162Hom.: 6426 Cov.: 33 AF XY: 0.281 AC XY: 20862AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at