chr4-148103262-G-A

Variant names:

• chr4-148103262-G-A
• rs11737660
• NM_000901.5:c.2799+10842C>T

Variant summary

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

The NM_000901.5(NR3C2):​c.2799+10842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,014 control chromosomes in the GnomAD database, including 3,864 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 0.19 (3864 hom., cov: 32)
• Consequence: NR3C2 NM_000901.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 10 publications found

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]

NR3C2 Gene-Disease associations (from GenCC):

• autosomal dominant pseudohypoaldosteronism type 1

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Illumina, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• pseudohyperaldosteronism type 2

  Inheritance: AD, Unknown Classification: LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000901.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR3C2	NM_000901.5	MANE Select	c.2799+10842C>T		intron	N/A	NP_000892.2
	NR3C2	NM_001437657.1		c.2811+10842C>T		intron	N/A	NP_001424586.1
	NR3C2	NM_001437654.1		c.2799+10842C>T		intron	N/A	NP_001424583.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR3C2	ENST00000358102.8	TSL:1 MANE Select	c.2799+10842C>T		intron	N/A	ENSP00000350815.3
	NR3C2	ENST00000512865.5	TSL:1	c.2448+10842C>T		intron	N/A	ENSP00000423510.1
	NR3C2	ENST00000511528.1	TSL:5	c.2811+10842C>T		intron	N/A	ENSP00000421481.1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29299 AN: 151896 Hom.: 3860 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.193 AC: 29304 AN: 152014 Hom.: 3864 Cov.: 32 AF XY: 0.198 AC XY: 14728 AN XY: 74300

African (AFR) AF: 0.0450 AC: 1867 AN: 41462

American (AMR) AF: 0.260 AC: 3968 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2869 AN: 5156

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4812

European-Finnish (FIN) AF: 0.303 AC: 3196 AN: 10544

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15134 AN: 67974

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.207 Hom.: 8105

Bravo AF: 0.186

Asia WGS AF: 0.355 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.72
PhyloP100		-0.12
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

Other links and lift over

dbSNP: rs11737660; hg19: chr4-149024413;