Variant rs886039795 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP5

The NM_152766.5(TMEM256):c.244_265del(p.Phe82GlufsTer31) variant causes a frameshift change. 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 links:

TMEM256-PLSCR3 (HGNC:):

TMEM256-PLSCR3 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

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	UniProt
TMEM256	NM_152766.5 linkuse as main transcript	c.244_265del	p.Phe82GlufsTer31	frameshift_variant	4/4	ENST00000302422.4
TMEM256-PLSCR3	NR_037719.1 linkuse as main transcript	n.164+494_164+515del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
TMEM256	ENST00000302422.4 linkuse as main transcript	c.244_265del	p.Phe82GlufsTer31	frameshift_variant	4/4	1	NM_152766.5	P1
TMEM256	ENST00000576017.1 linkuse as main transcript	c.249_270del		3_prime_UTR_variant	3/3	3
TMEM256	ENST00000575427.1 linkuse as main transcript	n.217_238del		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

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

Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre

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.