8-144450507-CAA-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_001330618.2(ZFTRAF1):c.1085_1086delTT(p.Phe362fs) variant causes a frameshift change. 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
ZFTRAF1
NM_001330618.2 frameshift
NM_001330618.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.26
Genes affected
ZFTRAF1 (HGNC:17806): (zinc finger TRAF-type containing 1) Predicted to enable zinc ion binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
ENSG00000291316 (HGNC:56752): (TMEM276-ZFTRAF1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring LOC84773 and cysteine and histidine rich 1 (CYHR1). It encodes a fusion protein that shares sequence identity with proteins encoded by both independent genes. [provided by RefSeq, Feb 2022]
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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 8-144450507-CAA-C is Pathogenic according to our data. Variant chr8-144450507-CAA-C is described in ClinVar as [Pathogenic]. Clinvar id is 2446444.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFTRAF1 | ENST00000530374.6 | c.1085_1086delTT | p.Phe362fs | frameshift_variant | 4/4 | 3 | NM_001330618.2 | ENSP00000433769.1 | ||
ENSG00000291316 | ENST00000438911.6 | c.959_960delTT | p.Phe320fs | frameshift_variant | 5/5 | 2 | ENSP00000387426.2 | |||
ZFTRAF1 | ENST00000528663.1 | n.4894_4895delTT | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Neurodevelopmental disorder with hypotonia and gross motor and speech delay Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Cologne Center for Genomics, Faculty of Medicine, University of Cologne | - | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.