rs564260248
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_014844.5(TECPR2):c.952-18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000867 in 148,724 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00087 ( 1 hom., cov: 30)
Exomes 𝑓: 0.00082 ( 6 hom. )
Failed GnomAD Quality Control
Consequence
TECPR2
NM_014844.5 intron
NM_014844.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0380
Genes affected
TECPR2 (HGNC:19957): (tectonin beta-propeller repeat containing 2) The protein encoded by this gene is a member of the tectonin beta-propeller repeat-containing (TECPR) family, and contains both TECPR and tryptophan-aspartic acid repeat (WD repeat) domains. This gene has been implicated in autophagy, as reduced expression levels of this gene have been associated with impaired autophagy. Recessive mutations in this gene have been associated with a hereditary form of spastic paraparesis (HSP). HSP is characterized by progressive spasticity and paralysis of the legs. There is also some evidence linking mutations in this gene with birdshot chorioretinopathy (BSCR), which results in inflammation of the choroid and retina. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 14-102428232-T-G is Benign according to our data. Variant chr14-102428232-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 445658.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-102428232-T-G is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000867 (129/148724) while in subpopulation EAS AF= 0.0169 (86/5090). AF 95% confidence interval is 0.014. There are 1 homozygotes in gnomad4. There are 57 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.952-18T>G | intron_variant | ENST00000359520.12 | |||
TECPR2 | NM_001172631.3 | c.952-18T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.952-18T>G | intron_variant | 1 | NM_014844.5 | P1 | |||
TECPR2 | ENST00000558678.1 | c.952-18T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000875 AC: 130AN: 148628Hom.: 1 Cov.: 30
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GnomAD3 exomes AF: 0.00427 AC: 248AN: 58120Hom.: 1 AF XY: 0.00408 AC XY: 118AN XY: 28928
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000815 AC: 990AN: 1214170Hom.: 6 Cov.: 28 AF XY: 0.000798 AC XY: 469AN XY: 587786
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.000867 AC: 129AN: 148724Hom.: 1 Cov.: 30 AF XY: 0.000786 AC XY: 57AN XY: 72528
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 15, 2022 | See Variant Classification Assertion Criteria. - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 05, 2017 | - - |
Hereditary spastic paraplegia 49 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at