chr17-7403142-CCACTCAGAGCCTGGTAGTAAAA-C

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

Scores

Not classified

Clinical Significance

Likely pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 5.02
Variant links:
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
TMEM256NM_152766.5 linkuse as main transcriptc.244_265delTTTTACTACCAGGCTCTGAGTG p.Phe82fs frameshift_variant 4/4 ENST00000302422.4 NP_689979.1 Q8N2U0
TMEM256-PLSCR3NR_037719.1 linkuse as main transcriptn.164+494_164+515delTTTTACTACCAGGCTCTGAGTG intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TMEM256ENST00000302422.4 linkuse as main transcriptc.244_265delTTTTACTACCAGGCTCTGAGTG p.Phe82fs frameshift_variant 4/41 NM_152766.5 ENSP00000301939.3 Q8N2U0
TMEM256-PLSCR3ENST00000573331.5 linkuse as main transcriptn.198+146_198+167delTTTTACTACCAGGCTCTGAGTG intron_variant 2 ENSP00000466104.1 K7ERE1

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
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 providedresearchCenter for Genomic Medicine, King Faisal Specialist Hospital and Research Center-LOF, autozygosity mapping -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs886039795; hg19: chr17-7306461; API