rs1555162597
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1PP5
The NM_004302.5(ACVR1B):c.1262-502_1392+24del variant causes a splice acceptor, splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
ACVR1B
NM_004302.5 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
NM_004302.5 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.16
Genes affected
ACVR1B (HGNC:172): (activin A receptor type 1B) This gene encodes an activin A type IB receptor. Activins are dimeric growth and differentiation factors which belong to the transforming growth factor-beta (TGF-beta) superfamily of structurally related signaling proteins. Activins signal through a heteromeric complex of receptor serine kinases which include at least two type I and two type II receptors. This protein is a type I receptor which is essential for signaling. Mutations in this gene are associated with pituitary tumors. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PVS1
?
Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PP5
?
Variant 12-51991356-TGGCTATGAAAAAAAATGTTCCTGGCTACTCTTTTGTATTTCTTTTTGTTTAGTTGTTTTGTTTGAGACAGAGTCTTGCACTCTTGTCCAGGCTGGAGTGCAGTGGCATGATCTCTGCTCACTGCAACCTCTGCCTCCAGGGTTCAAGCTATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGTGTTTGCCACCATGCCTGGTTAATTTTTGTATTTTTAGTAGAGATGGGGTTTTACCGTGTTGGCGGGGCTGGTTTCAAACTACTGATCTCAGGTGATCCGCTTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCATGCCCGGCCCCTTTTGTGTATTTCTTGTTCCATACTTAGAATTAACTAACTTTCTAAGGAACCTTAGGGGGTAGTGGTATTTACAGAGCACAGTGTAGGTTTTGTCACCGGCTTCTGAGTAATCTTTTCCTGCTGTTGATAACTCAGGTAGATACTTTCTTTTCTCCCAGGAGTCCATGAAGAATATCAGCTGCCATATTACGACTTAGTGCCCTCTGACCCTTCCATTGAGGAAATGCGAAAGGTTGTATGTGATCAGAAGCTGCGTCCCAACATCCCCAACTGGTGGCAGAGTTATGAGGTAAGAAGCTGGCCTCCTGC-T is Pathogenic according to our data. Variant chr12-51991356-TGGCTATGAAAAAAAATGTTCCTGGCTACTCTTTTGTATTTCTTTTTGTTTAGTTGTTTTGTTTGAGACAGAGTCTTGCACTCTTGTCCAGGCTGGAGTGCAGTGGCATGATCTCTGCTCACTGCAACCTCTGCCTCCAGGGTTCAAGCTATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGTGTTTGCCACCATGCCTGGTTAATTTTTGTATTTTTAGTAGAGATGGGGTTTTACCGTGTTGGCGGGGCTGGTTTCAAACTACTGATCTCAGGTGATCCGCTTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCATGCCCGGCCCCTTTTGTGTATTTCTTGTTCCATACTTAGAATTAACTAACTTTCTAAGGAACCTTAGGGGGTAGTGGTATTTACAGAGCACAGTGTAGGTTTTGTCACCGGCTTCTGAGTAATCTTTTCCTGCTGTTGATAACTCAGGTAGATACTTTCTTTTCTCCCAGGAGTCCATGAAGAATATCAGCTGCCATATTACGACTTAGTGCCCTCTGACCCTTCCATTGAGGAAATGCGAAAGGTTGTATGTGATCAGAAGCTGCGTCCCAACATCCCCAACTGGTGGCAGAGTTATGAGGTAAGAAGCTGGCCTCCTGC-T is described in ClinVar as [Pathogenic]. Clinvar id is 8228.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACVR1B | NM_004302.5 | c.1262-502_1392+24del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 8/9 | ENST00000257963.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACVR1B | ENST00000257963.9 | c.1262-502_1392+24del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 8/9 | 1 | NM_004302.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Carcinoma of pancreas Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 13, 2001 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at