rs2763

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001164760.2(PRKAR1B):​c.*407G>T variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PRKAR1B
NM_001164760.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Publications

11 publications found
Variant links:
Genes affected
PRKAR1B (HGNC:9390): (protein kinase cAMP-dependent type I regulatory subunit beta) The protein encoded by this gene is a regulatory subunit of cyclic AMP-dependent protein kinase A (PKA), which is involved in the signaling pathway of the second messenger cAMP. Two regulatory and two catalytic subunits form the PKA holoenzyme, disbands after cAMP binding. The holoenzyme is involved in many cellular events, including ion transport, metabolism, and transcription. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2015]
PRKAR1B Gene-Disease associations (from GenCC):
  • Marbach-Schaaf neurodevelopmental syndrome
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • PRKAR1B-related neurodegenerative dementia with intermediate filaments
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164760.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRKAR1B
NM_001164760.2
MANE Select
c.*407G>T
3_prime_UTR
Exon 11 of 11NP_001158232.1
PRKAR1B
NM_001164758.2
c.*407G>T
3_prime_UTR
Exon 11 of 11NP_001158230.1
PRKAR1B
NM_001164759.1
c.*407G>T
3_prime_UTR
Exon 11 of 11NP_001158231.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRKAR1B
ENST00000537384.6
TSL:5 MANE Select
c.*407G>T
3_prime_UTR
Exon 11 of 11ENSP00000440449.1
PRKAR1B
ENST00000360274.8
TSL:1
c.*407G>T
3_prime_UTR
Exon 11 of 11ENSP00000353415.4
PRKAR1B
ENST00000403562.5
TSL:1
c.*407G>T
3_prime_UTR
Exon 11 of 11ENSP00000385349.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
39410
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
20678
African (AFR)
AF:
0.00
AC:
0
AN:
478
American (AMR)
AF:
0.00
AC:
0
AN:
3086
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
796
East Asian (EAS)
AF:
0.00
AC:
0
AN:
906
South Asian (SAS)
AF:
0.00
AC:
0
AN:
5910
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
1722
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
126
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
24322
Other (OTH)
AF:
0.00
AC:
0
AN:
2064
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
29
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.4
DANN
Benign
0.56
PhyloP100
-0.076

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs2763; hg19: chr7-589660; API