21-14964954-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003489.4(NRIP1):c.3239C>T(p.Thr1080Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003489.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRIP1 | NM_003489.4 | c.3239C>T | p.Thr1080Ile | missense_variant | 4/4 | ENST00000318948.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRIP1 | ENST00000318948.7 | c.3239C>T | p.Thr1080Ile | missense_variant | 4/4 | 2 | NM_003489.4 | P1 | |
NRIP1 | ENST00000400199.5 | c.3239C>T | p.Thr1080Ile | missense_variant | 3/3 | 3 | P1 | ||
NRIP1 | ENST00000400202.5 | c.3239C>T | p.Thr1080Ile | missense_variant | 3/3 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251074Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135692
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461630Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727112
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.3239C>T (p.T1080I) alteration is located in exon 4 (coding exon 1) of the NRIP1 gene. This alteration results from a C to T substitution at nucleotide position 3239, causing the threonine (T) at amino acid position 1080 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at