19-35825976-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004646.4(NPHS1):c.*538G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 152,568 control chromosomes in the GnomAD database, including 536 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (530 hom., cov: 32)
  • Exomes 𝑓: 0.089 (6 hom.)
• Consequence: NPHS1 NM_004646.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.07

Genes affected

NPHS1 (HGNC:7908): (NPHS1 adhesion molecule, nephrin) This gene encodes a member of the immunoglobulin family of cell adhesion molecules that functions in the glomerular filtration barrier in the kidney. The gene is primarily expressed in renal tissues, and the protein is a type-1 transmembrane protein found at the slit diaphragm of glomerular podocytes. The slit diaphragm is thought to function as an ultrafilter to exclude albumin and other plasma macromolecules in the formation of urine. Mutations in this gene result in Finnish-type congenital nephrosis 1, characterized by severe proteinuria and loss of the slit diaphragm and foot processes.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 19-35825976-C-T is Benign according to our data. Variant chr19-35825976-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 328848.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPHS1	NM_004646.4	c.*538G>A		3_prime_UTR_variant	29/29	ENST00000378910.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPHS1	ENST00000378910.10	c.*538G>A		3_prime_UTR_variant	29/29	1	NM_004646.4	P2

Frequencies

GnomAD3 genomes AF: 0.0733 AC: 11135 AN: 151936 Hom.: 530 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0869

GnomAD4 exome AF: 0.0895 AC: 46 AN: 514 Hom.: 6 Cov.: 0 AF XY: 0.0899 AC XY: 25 AN XY: 278

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0481

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.146

Gnomad4 NFE exome AF: 0.0982

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.0732 AC: 11136 AN: 152054 Hom.: 530 Cov.: 32 AF XY: 0.0730 AC XY: 5423 AN XY: 74308

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.000582

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0859

Alfa AF: 0.0264 Hom.: 15

Bravo AF: 0.0682

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital nephrotic syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.53
Dann	Benign	0.87

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: rs71354105; hg19: chr19-36316878;