rs147641617
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_004646.4(NPHS1):c.1747G>A(p.Glu583Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,613,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. E583E) has been classified as Likely benign.
Frequency
Consequence
NM_004646.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHS1 | NM_004646.4 | c.1747G>A | p.Glu583Lys | missense_variant | 13/29 | ENST00000378910.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHS1 | ENST00000378910.10 | c.1747G>A | p.Glu583Lys | missense_variant | 13/29 | 1 | NM_004646.4 | P2 | |
NPHS1 | ENST00000353632.6 | c.1747G>A | p.Glu583Lys | missense_variant | 13/28 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000539 AC: 82AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 249710Hom.: 0 AF XY: 0.0000962 AC XY: 13AN XY: 135148
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461468Hom.: 0 Cov.: 34 AF XY: 0.0000495 AC XY: 36AN XY: 727000
GnomAD4 genome AF: 0.000538 AC: 82AN: 152364Hom.: 0 Cov.: 32 AF XY: 0.000604 AC XY: 45AN XY: 74512
ClinVar
Submissions by phenotype
Finnish congenital nephrotic syndrome Uncertain:3
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Sep 29, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at