rs1555879360
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_003489.4(NRIP1):c.279del(p.Trp93Ter) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
NRIP1
NM_003489.4 frameshift
NM_003489.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.57
Genes affected
NRIP1 (HGNC:8001): (nuclear receptor interacting protein 1) Nuclear receptor interacting protein 1 (NRIP1) is a nuclear protein that specifically interacts with the hormone-dependent activation domain AF2 of nuclear receptors. Also known as RIP140, this protein modulates transcriptional activity of the estrogen receptor. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 21-14967913-TC-T is Pathogenic according to our data. Variant chr21-14967913-TC-T is described in ClinVar as [Pathogenic]. Clinvar id is 548653.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRIP1 | NM_003489.4 | c.279del | p.Trp93Ter | frameshift_variant | 4/4 | ENST00000318948.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRIP1 | ENST00000318948.7 | c.279del | p.Trp93Ter | frameshift_variant | 4/4 | 2 | NM_003489.4 | P1 | |
NRIP1 | ENST00000400199.5 | c.279del | p.Trp93Ter | frameshift_variant | 3/3 | 3 | P1 | ||
NRIP1 | ENST00000400202.5 | c.279del | p.Trp93Ter | frameshift_variant | 3/3 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 35
GnomAD4 exome
Cov.:
35
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Congenital anomaly of kidney and urinary tract Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Aug 24, 2018 | - - |
Pathogenic, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Apr 05, 2017 | - - |
Congenital anomalies of kidney and urinary tract 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 09, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at