4-148079614-A-AAGAT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000901.5(NR3C2):c.*1729_*1730insATCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00546 in 152,310 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0055 ( 11 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NR3C2
NM_000901.5 3_prime_UTR
NM_000901.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.94
Genes affected
NR3C2 (HGNC:7979): (nuclear receptor subfamily 3 group C member 2) This gene encodes the mineralocorticoid receptor, which mediates aldosterone actions on salt and water balance within restricted target cells. The protein functions as a ligand-dependent transcription factor that binds to mineralocorticoid response elements in order to transactivate target genes. Mutations in this gene cause autosomal dominant pseudohypoaldosteronism type I, a disorder characterized by urinary salt wasting. Defects in this gene are also associated with early onset hypertension with severe exacerbation in pregnancy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 4-148079614-A-AAGAT is Benign according to our data. Variant chr4-148079614-A-AAGAT is described in ClinVar as [Likely_benign]. Clinvar id is 347686.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 (831/152310) while in subpopulation AFR AF= 0.0187 (776/41568). AF 95% confidence interval is 0.0176. There are 11 homozygotes in gnomad4. There are 383 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 811 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR3C2 | NM_000901.5 | c.*1729_*1730insATCT | 3_prime_UTR_variant | 9/9 | ENST00000358102.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR3C2 | ENST00000358102.8 | c.*1729_*1730insATCT | 3_prime_UTR_variant | 9/9 | 1 | NM_000901.5 | P4 | ||
NR3C2 | ENST00000344721.8 | c.*1729_*1730insATCT | 3_prime_UTR_variant | 9/9 | 5 | P4 | |||
NR3C2 | ENST00000625323.2 | c.*1729_*1730insATCT | 3_prime_UTR_variant | 9/9 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00533 AC: 811AN: 152192Hom.: 9 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 432Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 260
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GnomAD4 genome ? AF: 0.00546 AC: 831AN: 152310Hom.: 11 Cov.: 33 AF XY: 0.00514 AC XY: 383AN XY: 74490
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal dominant pseudohypoaldosteronism type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at