rs77533254
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_153240.5(NPHP3):c.1986G>T(p.Arg662Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000763 in 1,441,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Synonymous variant affecting the same amino acid position (i.e. R662R) has been classified as Likely benign.
Frequency
Consequence
NM_153240.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHP3 | NM_153240.5 | c.1986G>T | p.Arg662Ser | missense_variant, splice_region_variant | 14/27 | ENST00000337331.10 | |
NPHP3-ACAD11 | NR_037804.1 | n.1992G>T | splice_region_variant, non_coding_transcript_exon_variant | 13/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHP3 | ENST00000337331.10 | c.1986G>T | p.Arg662Ser | missense_variant, splice_region_variant | 14/27 | 1 | NM_153240.5 | P1 | |
NPHP3 | ENST00000490993.5 | n.1664G>T | splice_region_variant, non_coding_transcript_exon_variant | 10/23 | 5 | ||||
NPHP3 | ENST00000465756.5 | c.1594G>T | p.Val532Phe | missense_variant, splice_region_variant, NMD_transcript_variant | 13/25 | 5 | |||
NPHP3 | ENST00000684294.1 | c.1594G>T | p.Val532Phe | missense_variant, splice_region_variant, NMD_transcript_variant | 13/25 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248506Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134584
GnomAD4 exome AF: 0.00000763 AC: 11AN: 1441250Hom.: 0 Cov.: 27 AF XY: 0.00000835 AC XY: 6AN XY: 718480
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at