Variant chr11-66295133-TGTCGTGGCCCCTGCGC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The NM_153266.4(TMEM151A):c.897_912del(p.Leu300ProfsTer118) variant causes a frameshift 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 Pathogenic (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

TMEM151A
NM_153266.4 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 7.81

Variant links:

Genes affected

TMEM151A (HGNC:28497): (transmembrane protein 151A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM151A links:

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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 11-66295133-TGTCGTGGCCCCTGCGC-T is Pathogenic according to our data. Variant chr11-66295133-TGTCGTGGCCCCTGCGC-T is described in ClinVar as [Pathogenic]. Clinvar id is 2443876.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM151A	NM_153266.4 linkuse as main transcript	c.897_912del	p.Leu300ProfsTer118	frameshift_variant	2/2	ENST00000327259.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM151A	ENST00000327259.5 linkuse as main transcript	c.897_912del	p.Leu300ProfsTer118	frameshift_variant	2/2	1	NM_153266.4	P1

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: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Episodic kinesigenic dyskinesia 3

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Feb 15, 2023

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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

No publications associated with this variant yet.