chr17-68512540-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002734.5(PRKAR1A):c.-15C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002734.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Publications
- Acrodysostosis 1 with or without hormone resistanceInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- acrodysostosis with multiple hormone resistanceInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Illumina, Orphanet
- Carney complex, type 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- pigmented nodular adrenocortical disease, primary, 1Inheritance: AD Classification: STRONG, MODERATE Submitted by: Genomics England PanelApp, Ambry Genetics
- acrodysostosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Carney complexInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial atrial myxomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- primary pigmented nodular adrenocortical diseaseInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRKAR1A | NM_002734.5 | c.-15C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 11 | ENST00000589228.6 | NP_002725.1 | ||
PRKAR1A | NM_002734.5 | c.-15C>T | 5_prime_UTR_variant | Exon 1 of 11 | ENST00000589228.6 | NP_002725.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKAR1A | ENST00000589228.6 | c.-15C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 11 | 1 | NM_002734.5 | ENSP00000464977.2 | |||
PRKAR1A | ENST00000589228.6 | c.-15C>T | 5_prime_UTR_variant | Exon 1 of 11 | 1 | NM_002734.5 | ENSP00000464977.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2500Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 1756
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Carney complex, type 1 Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 1396471). This variant has not been reported in the literature in individuals affected with PRKAR1A-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant occurs in a non-coding region of the PRKAR1A gene. It does not change the encoded amino acid sequence of the PRKAR1A protein. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at