rs743572
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000102(CYP17A1):c.-34T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151974 control chromosomes in the gnomAD Genomes database, including 11760 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (β β ).
Frequency
Genomes: π 0.39 ( 11760 hom., cov: 32)
Exomes π: 0.40 ( 19776 hom. )
Consequence
CYP17A1
NM_000102 5_prime_UTR
NM_000102 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.520
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 10:102837395-A>G is Benign according to our data. Variant chr10-102837395-A-G is described in ClinVar as [Benign]. Clinvar id is 298630. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-102837395-A-G is described in Lovd as [Benign].
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP17A1 | NM_000102.4 | c.-34T>C | 5_prime_UTR_variant | 1/8 | ENST00000369887.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP17A1 | ENST00000369887.4 | c.-34T>C | 5_prime_UTR_variant | 1/8 | 1 | NM_000102.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.391 AC: 59374AN: 151974Hom.: 11760 Cov.: 32
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GnomAD3 exomes AF: 0.398 AC: 98034AN: 246120Hom.: 19776 AF XY: 0.396 AC XY: 52888AN XY: 133508
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 04, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 25929975, 24629213, 7849715, 20113968, 16998812, 17307805, 19013303, 21716904, 20133979, 17606708, 9067272, 20798986) - |
Deficiency of steroid 17-alpha-monooxygenase Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
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Cadd
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Dann
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at