rs61741547
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_020921.4(NIN):āc.5188T>Cā(p.Leu1730Leu) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,606,684 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 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_020921.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NIN | NM_020921.4 | c.5188T>C | p.Leu1730Leu | splice_region_variant, synonymous_variant | 24/31 | ENST00000530997.7 | NP_065972.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NIN | ENST00000530997.7 | c.5188T>C | p.Leu1730Leu | splice_region_variant, synonymous_variant | 24/31 | 5 | NM_020921.4 | ENSP00000436092.2 |
Frequencies
GnomAD3 genomes AF: 0.00691 AC: 1052AN: 152178Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.00166 AC: 416AN: 251290Hom.: 7 AF XY: 0.00122 AC XY: 166AN XY: 135826
GnomAD4 exome AF: 0.000672 AC: 977AN: 1454388Hom.: 14 Cov.: 27 AF XY: 0.000592 AC XY: 429AN XY: 724052
GnomAD4 genome AF: 0.00691 AC: 1053AN: 152296Hom.: 22 Cov.: 32 AF XY: 0.00653 AC XY: 486AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 18, 2014 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
NIN-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 04, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at