rs906888001
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_004646.4(NPHS1):c.1170+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,612,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004646.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHS1 | NM_004646.4 | c.1170+7C>T | splice_region_variant, intron_variant | ENST00000378910.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHS1 | ENST00000378910.10 | c.1170+7C>T | splice_region_variant, intron_variant | 1 | NM_004646.4 | P2 | |||
NPHS1 | ENST00000353632.6 | c.1170+7C>T | splice_region_variant, intron_variant | 5 | A2 | ||||
NPHS1 | ENST00000592132.1 | n.177+7C>T | splice_region_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151780Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250258Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135530
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460822Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726720
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151780Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74100
ClinVar
Submissions by phenotype
Finnish congenital nephrotic syndrome Pathogenic:1Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 06, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | May 05, 2017 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jan 07, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at