rs1554708715
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006808.3(SEC61B):c.106_107dup(p.Asn36LysfsTer42) variant causes a frameshift, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
SEC61B
NM_006808.3 frameshift, splice_region
NM_006808.3 frameshift, splice_region
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.91
Genes affected
SEC61B (HGNC:16993): (SEC61 translocon subunit beta) The Sec61 complex is the central component of the protein translocation apparatus of the endoplasmic reticulum (ER) membrane. Oligomers of the Sec61 complex form a transmembrane channel where proteins are translocated across and integrated into the ER membrane. This complex consists of three membrane proteins- alpha, beta, and gamma. This gene encodes the beta-subunit protein. The Sec61 subunits are also observed in the post-ER compartment, suggesting that these proteins can escape the ER and recycle back. There is evidence for multiple polyadenylated sites for this transcript. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| SEC61B | NM_006808.3 | c.106_107dup | p.Asn36LysfsTer42 | frameshift_variant, splice_region_variant | 3/4 | ENST00000223641.5 | |
| SEC61B | XM_047422662.1 | c.59_60dup | p.Cys21AsnfsTer62 | frameshift_variant, splice_region_variant | 2/3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SEC61B | ENST00000223641.5 | c.106_107dup | p.Asn36LysfsTer42 | frameshift_variant, splice_region_variant | 3/4 | 1 | NM_006808.3 | P1 | |
| SEC61B | ENST00000498603.5 | c.-57_-56dup | splice_region_variant, 5_prime_UTR_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
| Uncertain significance, no assertion criteria provided | literature only | OMIM | Feb 21, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at