rs1555162597

Variant names:

• chr12-51991356-TGGCTATGAAAAAAAATGTTCCTGGCTACTCTTTTGTATTTCTTTTTGTTTAGTTGTTTTGTTTGAGACAGAGTCTTGCACTCTTGTCCAGGCTGGAGTGCAGTGGCATGATCTCTGCTCACTGCAACCTCTGCCTCCAGGGTTCAAGCTATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGTGTTTGCCACCATGCCTGGTTAATTTTTGTATTTTTAGTAGAGATGGGGTTTTACCGTGTTGGCGGGGCTGGTTTCAAACTACTGATCTCAGGTGATCCGCTTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCATGCCCGGCCCCTTTTGTGTATTTCTTGTTCCATACTTAGAATTAACTAACTTTCTAAGGAACCTTAGGGGGTAGTGGTATTTACAGAGCACAGTGTAGGTTTTGTCACCGGCTTCTGAGTAATCTTTTCCTGCTGTTGATAACTCAGGTAGATACTTTCTTTTCTCCCAGGAGTCCATGAAGAATATCAGCTGCCATATTACGACTTAGTGCCCTCTGACCCTTCCATTGAGGAAATGCGAAAGGTTGTATGTGATCAGAAGCTGCGTCCCAACATCCCCAACTGGTGGCAGAGTTATGAGGTAAGAAGCTGGCCTCCTGC-T
• rs1555162597
• NM_004302.5:c.1262-502_1392+24del

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PVS1_Strong 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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Publications: 0 publications found

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]

ACVR1B Gene-Disease associations (from GenCC):

• malignant pancreatic neoplasm

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 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.
• 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 rank	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	Exon 8 of 9	ENST00000257963.9	NP_004293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACVR1B	ENST00000257963.9	c.1262-506_1392+20del		exon_loss_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 8 of 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

Mar 13, 2001

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1555162597; hg19: chr12-52385140;