3-132721945-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_153240.5(NPHP3):c.393+18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,611,062 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 Likely benign (★★).
Frequency
Consequence
NM_153240.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPHP3 | NM_153240.5 | c.393+18C>T | intron_variant | Intron 1 of 26 | ENST00000337331.10 | NP_694972.3 | ||
NPHP3-AS1 | NR_002811.2 | n.196G>A | non_coding_transcript_exon_variant | Exon 1 of 11 | ||||
NPHP3-AS1 | NR_152743.1 | n.196G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | ||||
NPHP3-ACAD11 | NR_037804.1 | n.497+18C>T | intron_variant | Intron 1 of 44 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000145 AC: 35AN: 240680Hom.: 0 AF XY: 0.0000832 AC XY: 11AN XY: 132268
GnomAD4 exome AF: 0.0000782 AC: 114AN: 1458726Hom.: 0 Cov.: 31 AF XY: 0.0000813 AC XY: 59AN XY: 725714
GnomAD4 genome AF: 0.000381 AC: 58AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Nephronophthisis 3;C2673885:NPHP3-related Meckel-like syndrome;C3715199:Renal-hepatic-pancreatic dysplasia 1 Benign:1
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Nephronophthisis Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at