chr17-7403142-CCACTCAGAGCCTGGTAGTAAAA-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_152766.5(TMEM256):c.244_265delTTTTACTACCAGGCTCTGAGTG(p.Phe82fs) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
TMEM256
NM_152766.5 frameshift
NM_152766.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.02
Genes affected
TMEM256 (HGNC:28618): (transmembrane protein 256) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
TMEM256-PLSCR3 (HGNC:49186): (TMEM256-PLSCR3 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring chromosome 17 open reading frame 61 (C17orf61) and phospholipid scramblase 3 (PLSCR3) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-7403142-CCACTCAGAGCCTGGTAGTAAAA-C is Pathogenic according to our data. Variant chr17-7403142-CCACTCAGAGCCTGGTAGTAAAA-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 266078.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM256 | NM_152766.5 | c.244_265delTTTTACTACCAGGCTCTGAGTG | p.Phe82fs | frameshift_variant | 4/4 | ENST00000302422.4 | NP_689979.1 | |
TMEM256-PLSCR3 | NR_037719.1 | n.164+494_164+515delTTTTACTACCAGGCTCTGAGTG | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM256 | ENST00000302422.4 | c.244_265delTTTTACTACCAGGCTCTGAGTG | p.Phe82fs | frameshift_variant | 4/4 | 1 | NM_152766.5 | ENSP00000301939.3 | ||
TMEM256-PLSCR3 | ENST00000573331.5 | n.198+146_198+167delTTTTACTACCAGGCTCTGAGTG | intron_variant | 2 | ENSP00000466104.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Asphyxiating thoracic dystrophy 3 Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | - | LOF, autozygosity mapping - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at