4-64280982-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001010874.5(TECRL):c.964+59T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 1,280,848 control chromosomes in the GnomAD database, including 569,650 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.85 ( 57579 hom., cov: 32)
Exomes 𝑓: 0.95 ( 512071 hom. )
Consequence
TECRL
NM_001010874.5 intron
NM_001010874.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.287
Genes affected
TECRL (HGNC:27365): (trans-2,3-enoyl-CoA reductase like) The protein encoded by this gene contains a ubiquitin-like domain in the N-terminal region, three transmembrane segments and a C-terminal 3-oxo-5-alpha steroid 4-dehydrogenase domain. The protein belongs to the steroid 5-alpha reductase family. Mutations in this gene result in ventricular tachycardia, catecholaminergic polymorphic, 3. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 4-64280982-A-G is Benign according to our data. Variant chr4-64280982-A-G is described in ClinVar as [Benign]. Clinvar id is 1221036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECRL | NM_001010874.5 | c.964+59T>C | intron_variant | ENST00000381210.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECRL | ENST00000381210.8 | c.964+59T>C | intron_variant | 1 | NM_001010874.5 | P1 | |||
TECRL | ENST00000511997.1 | c.63+492T>C | intron_variant | 1 | |||||
TECRL | ENST00000507440.5 | c.964+59T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.855 AC: 129842AN: 151888Hom.: 57580 Cov.: 32
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GnomAD4 exome AF: 0.950 AC: 1072867AN: 1128842Hom.: 512071 AF XY: 0.952 AC XY: 543941AN XY: 571074
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GnomAD4 genome AF: 0.854 AC: 129870AN: 152006Hom.: 57579 Cov.: 32 AF XY: 0.860 AC XY: 63873AN XY: 74302
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at