chr19-35851310-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004646.4(NPHS1):āc.349G>Cā(p.Glu117Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,532 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E117K) has been classified as Benign.
Frequency
Consequence
NM_004646.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHS1 | NM_004646.4 | c.349G>C | p.Glu117Gln | missense_variant | 3/29 | ENST00000378910.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHS1 | ENST00000378910.10 | c.349G>C | p.Glu117Gln | missense_variant | 3/29 | 1 | NM_004646.4 | P2 | |
NPHS1 | ENST00000353632.6 | c.349G>C | p.Glu117Gln | missense_variant | 3/28 | 5 | A2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249994Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135268
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461532Hom.: 0 Cov.: 54 AF XY: 0.00000138 AC XY: 1AN XY: 727036
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at