rs117833765
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The ENST00000215567.10(TECR):c.552C>T(p.Tyr184=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,613,980 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00035 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00076 ( 14 hom. )
Consequence
TECR
ENST00000215567.10 synonymous
ENST00000215567.10 synonymous
Scores
9
Clinical Significance
Conservation
PhyloP100: 0.534
Genes affected
TECR (HGNC:4551): (trans-2,3-enoyl-CoA reductase) This gene encodes a multi-pass membrane protein that resides in the endoplasmic reticulum, and belongs to the steroid 5-alpha reductase family. The elongation of microsomal long and very long chain fatty acid consists of 4 sequential reactions. This protein catalyzes the final step, reducing trans-2,3-enoyl-CoA to saturated acyl-CoA. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Apr 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.009176761).
BP6
Variant 19-14564848-C-T is Benign according to our data. Variant chr19-14564848-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 436973.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-14564848-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.534 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECR | NM_138501.6 | c.552C>T | p.Tyr184= | synonymous_variant | 8/13 | ENST00000215567.10 | NP_612510.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECR | ENST00000215567.10 | c.552C>T | p.Tyr184= | synonymous_variant | 8/13 | 1 | NM_138501.6 | ENSP00000215567 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152050Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.00127 AC: 320AN: 251416Hom.: 3 AF XY: 0.00178 AC XY: 242AN XY: 135912
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GnomAD4 exome AF: 0.000760 AC: 1111AN: 1461812Hom.: 14 Cov.: 34 AF XY: 0.00110 AC XY: 798AN XY: 727202
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GnomAD4 genome AF: 0.000355 AC: 54AN: 152168Hom.: 0 Cov.: 30 AF XY: 0.000511 AC XY: 38AN XY: 74374
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | TECR: BP4, BP7, BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 05, 2016 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
D;D
Sift4G
Benign
T
MVP
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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