rs758238787
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_153240.5(NPHP3):āc.3129T>Cā(p.Tyr1043=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000175 in 1,144,144 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_153240.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHP3 | NM_153240.5 | c.3129T>C | p.Tyr1043= | synonymous_variant | 22/27 | ENST00000337331.10 | |
NPHP3-ACAD11 | NR_037804.1 | n.3135T>C | non_coding_transcript_exon_variant | 21/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHP3 | ENST00000337331.10 | c.3129T>C | p.Tyr1043= | synonymous_variant | 22/27 | 1 | NM_153240.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000422 AC: 1AN: 237158Hom.: 0 AF XY: 0.00000777 AC XY: 1AN XY: 128700
GnomAD4 exome AF: 0.00000175 AC: 2AN: 1144144Hom.: 0 Cov.: 18 AF XY: 0.00000343 AC XY: 2AN XY: 582810
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at