chr4-64281161-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001010874.5(TECRL):c.919-75A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,140,748 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0055 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00053 ( 5 hom. )
Consequence
TECRL
NM_001010874.5 intron
NM_001010874.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.575
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 4-64281161-T-C is Benign according to our data. Variant chr4-64281161-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1187411.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00546 (830/152090) while in subpopulation AFR AF= 0.019 (790/41544). AF 95% confidence interval is 0.0179. There are 2 homozygotes in gnomad4. There are 391 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECRL | NM_001010874.5 | c.919-75A>G | intron_variant | ENST00000381210.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECRL | ENST00000381210.8 | c.919-75A>G | intron_variant | 1 | NM_001010874.5 | P1 | |||
TECRL | ENST00000511997.1 | c.63+313A>G | intron_variant | 1 | |||||
TECRL | ENST00000507440.5 | c.919-75A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00543 AC: 825AN: 151970Hom.: 2 Cov.: 32
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GnomAD4 exome AF: 0.000527 AC: 521AN: 988658Hom.: 5 AF XY: 0.000466 AC XY: 234AN XY: 502310
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GnomAD4 genome AF: 0.00546 AC: 830AN: 152090Hom.: 2 Cov.: 32 AF XY: 0.00526 AC XY: 391AN XY: 74340
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2018 | - - |
Computational scores
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Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at