chr9-124482676-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004959.5(NR5A1):c.*82C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,269,752 control chromosomes in the GnomAD database, including 163,539 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.57 ( 25776 hom., cov: 31)
Exomes 𝑓: 0.47 ( 137763 hom. )
Consequence
NR5A1
NM_004959.5 3_prime_UTR
NM_004959.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.188
Genes affected
NR5A1 (HGNC:7983): (nuclear receptor subfamily 5 group A member 1) The protein encoded by this gene is a transcriptional activator involved in sex determination. The encoded protein binds DNA as a monomer. Defects in this gene are a cause of XY sex reversal with or without adrenal failure as well as adrenocortical insufficiency without ovarian defect. [provided by RefSeq, Jul 2008]
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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=-0.82).
BP6
Variant 9-124482676-G-A is Benign according to our data. Variant chr9-124482676-G-A is described in ClinVar as [Benign]. Clinvar id is 701816.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-124482676-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR5A1 | NM_004959.5 | c.*82C>T | 3_prime_UTR_variant | 7/7 | ENST00000373588.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR5A1 | ENST00000373588.9 | c.*82C>T | 3_prime_UTR_variant | 7/7 | 1 | NM_004959.5 | P1 | ||
NR5A1 | ENST00000620110.4 | c.*82C>T | 3_prime_UTR_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.569 AC: 86290AN: 151588Hom.: 25733 Cov.: 31
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GnomAD4 exome AF: 0.473 AC: 528827AN: 1118054Hom.: 137763 Cov.: 17 AF XY: 0.476 AC XY: 265951AN XY: 558830
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GnomAD4 genome AF: 0.569 AC: 86389AN: 151698Hom.: 25776 Cov.: 31 AF XY: 0.570 AC XY: 42223AN XY: 74104
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ClinVar
Significance: Benign
Submissions summary: Benign:3
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 03, 2015 | This variant is associated with the following publications: (PMID: 23096908, 27884173, 29090230) - |
Oligosynaptic infertility;C2751824:46,XY disorder of sex development Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 03, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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