12-51991356-TGGCTATGAAAAAAAATGTTCCTGGCTACTCTTTTGTATTTCTTTTTGTTTAGTTGTTTTGTTTGAGACAGAGTCTTGCACTCTTGTCCAGGCTGGAGTGCAGTGGCATGATCTCTGCTCACTGCAACCTCTGCCTCCAGGGTTCAAGCTATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGTGTTTGCCACCATGCCTGGTTAATTTTTGTATTTTTAGTAGAGATGGGGTTTTACCGTGTTGGCGGGGCTGGTTTCAAACTACTGATCTCAGGTGATCCGCTTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCATGCCCGGCCCCTTTTGTGTATTTCTTGTTCCATACTTAGAATTAACTAACTTTCTAAGGAACCTTAGGGGGTAGTGGTATTTACAGAGCACAGTGTAGGTTTTGTCACCGGCTTCTGAGTAATCTTTTCCTGCTGTTGATAACTCAGGTAGATACTTTCTTTTCTCCCAGGAGTCCATGAAGAATATCAGCTGCCATATTACGACTTAGTGCCCTCTGACCCTTCCATTGAGGAAATGCGAAAGGTTGTATGTGATCAGAAGCTGCGTCCCAACATCCCCAACTGGTGGCAGAGTTATGAGGTAAGAAGCTGGCCTCCTGC-T

Position:

• chr12-51991356-TGGCTATGAAAAAAAATGTTCCTGGCTACTCTTTTGTATTTCTTTTTGTTTAGTTGTTTTGTTTGAGACAGAGTCTTGCACTCTTGTCCAGGCTGGAGTGCAGTGGCATGATCTCTGCTCACTGCAACCTCTGCCTCCAGGGTTCAAGCTATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGTGTTTGCCACCATGCCTGGTTAATTTTTGTATTTTTAGTAGAGATGGGGTTTTACCGTGTTGGCGGGGCTGGTTTCAAACTACTGATCTCAGGTGATCCGCTTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCATGCCCGGCCCCTTTTGTGTATTTCTTGTTCCATACTTAGAATTAACTAACTTTCTAAGGAACCTTAGGGGGTAGTGGTATTTACAGAGCACAGTGTAGGTTTTGTCACCGGCTTCTGAGTAATCTTTTCCTGCTGTTGATAACTCAGGTAGATACTTTCTTTTCTCCCAGGAGTCCATGAAGAATATCAGCTGCCATATTACGACTTAGTGCCCTCTGACCCTTCCATTGAGGAAATGCGAAAGGTTGTATGTGATCAGAAGCTGCGTCCCAACATCCCCAACTGGTGGCAGAGTTATGAGGTAAGAAGCTGGCCTCCTGC-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_Strong PM2 PP5

The NM_004302.5(ACVR1B):​c.1262-502_1392+24del variant causes a exon loss, splice acceptor, splice donor, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ACVR1B NM_004302.5 exon_loss, splice_acceptor, splice_donor, splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• 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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates 1.002635046113307 fraction of the gene. No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• 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	Protein	UniProt
ACVR1B	NM_004302.5	c.1262-502_1392+24del		exon_loss_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, intron_variant	8/9	ENST00000257963.9	NP_004293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACVR1B	ENST00000257963.9	c.1262-502_1392+24del		exon_loss_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, intron_variant	8/9	1	NM_004302.5	ENSP00000257963.4

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Carcinoma of pancreas Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 13, 2001

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555162597; hg19: chr12-52385140;