chr4-148298317-A-C

Variant names:

• chr4-148298317-A-C
• rs7689925
• NM_000901.5:c.1758-38200T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000901.5(NR3C2):​c.1758-38200T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,126 control chromosomes in the GnomAD database, including 46,910 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (46910 hom., cov: 32)
• Consequence: NR3C2 NM_000901.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR3C2	NM_000901.5	c.1758-38200T>G		intron_variant	Intron 2 of 8	ENST00000358102.8	NP_000892.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR3C2	ENST00000358102.8	c.1758-38200T>G		intron_variant	Intron 2 of 8	1	NM_000901.5	ENSP00000350815.3

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119127 AN: 152008 Hom.: 46868 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.779

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.784 AC: 119229 AN: 152126 Hom.: 46910 Cov.: 32 AF XY: 0.782 AC XY: 58128 AN XY: 74344

African (AFR) AF: 0.786 AC: 32609 AN: 41484

American (AMR) AF: 0.792 AC: 12117 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2830 AN: 3468

East Asian (EAS) AF: 0.844 AC: 4364 AN: 5172

South Asian (SAS) AF: 0.811 AC: 3914 AN: 4826

European-Finnish (FIN) AF: 0.705 AC: 7452 AN: 10570

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53209 AN: 67994

Other (OTH) AF: 0.781 AC: 1647 AN: 2110

Alfa AF: 0.780 Hom.: 22914

Bravo AF: 0.790

Asia WGS AF: 0.823 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.37
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7689925; hg19: chr4-149219469;