19-35843517-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004646.4(NPHS1):c.2289C>G(p.Val763Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,882 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V763V) has been classified as Benign.
Frequency
Consequence
NM_004646.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPHS1 | ENST00000378910.10 | c.2289C>G | p.Val763Val | synonymous_variant | Exon 17 of 29 | 1 | NM_004646.4 | ENSP00000368190.4 | ||
NPHS1 | ENST00000585400.1 | n.980C>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | |||||
NPHS1 | ENST00000353632.6 | c.2289C>G | p.Val763Val | synonymous_variant | Exon 17 of 28 | 5 | ENSP00000343634.5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251486Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135916
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461824Hom.: 1 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727224
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at