chr4-64280993-T-C
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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+48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.975 in 1,403,786 control chromosomes in the GnomAD database, including 666,972 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.97 ( 71215 hom., cov: 32)
Exomes 𝑓: 0.98 ( 595757 hom. )
Consequence
TECRL
NM_001010874.5 intron
NM_001010874.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.42
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=-0.95).
BP6
Variant 4-64280993-T-C is Benign according to our data. Variant chr4-64280993-T-C is described in ClinVar as [Benign]. Clinvar id is 1240736.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECRL | NM_001010874.5 | c.964+48A>G | intron_variant | ENST00000381210.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECRL | ENST00000381210.8 | c.964+48A>G | intron_variant | 1 | NM_001010874.5 | P1 | |||
TECRL | ENST00000511997.1 | c.63+481A>G | intron_variant | 1 | |||||
TECRL | ENST00000507440.5 | c.964+48A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.968 AC: 147051AN: 151944Hom.: 71181 Cov.: 32
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GnomAD3 exomes AF: 0.978 AC: 226337AN: 231468Hom.: 110677 AF XY: 0.979 AC XY: 122922AN XY: 125598
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GnomAD4 exome AF: 0.976 AC: 1221171AN: 1251724Hom.: 595757 Cov.: 15 AF XY: 0.976 AC XY: 614420AN XY: 629606
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GnomAD4 genome AF: 0.968 AC: 147144AN: 152062Hom.: 71215 Cov.: 32 AF XY: 0.968 AC XY: 71956AN XY: 74326
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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 | Mar 29, 2019 | - - |
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