rs72542742
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000394464.7(NR3C1):c.685G>A(p.Ala229Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,614,116 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000394464.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR3C1 | NM_000176.3 | c.685G>A | p.Ala229Thr | missense_variant | 2/9 | ENST00000394464.7 | NP_000167.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR3C1 | ENST00000394464.7 | c.685G>A | p.Ala229Thr | missense_variant | 2/9 | 1 | NM_000176.3 | ENSP00000377977 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00129 AC: 196AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00141 AC: 354AN: 250844Hom.: 1 AF XY: 0.00146 AC XY: 198AN XY: 135790
GnomAD4 exome AF: 0.00140 AC: 2053AN: 1461826Hom.: 2 Cov.: 32 AF XY: 0.00137 AC XY: 995AN XY: 727220
GnomAD4 genome AF: 0.00129 AC: 196AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.00137 AC XY: 102AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Glucocorticoid resistance Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at