rs41313507
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_020921.4(NIN):c.2987C>T(p.Ala996Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00381 in 1,614,162 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A996G) has been classified as Uncertain significance.
Frequency
Consequence
NM_020921.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIN | NM_020921.4 | c.2987C>T | p.Ala996Val | missense_variant | 18/31 | ENST00000530997.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIN | ENST00000530997.7 | c.2987C>T | p.Ala996Val | missense_variant | 18/31 | 5 | NM_020921.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00237 AC: 360AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00224 AC: 563AN: 251448Hom.: 0 AF XY: 0.00227 AC XY: 308AN XY: 135904
GnomAD4 exome AF: 0.00396 AC: 5795AN: 1461886Hom.: 17 Cov.: 42 AF XY: 0.00388 AC XY: 2820AN XY: 727246
GnomAD4 genome ? AF: 0.00237 AC: 361AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.00219 AC XY: 163AN XY: 74440
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2018 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 16, 2020 | - - |
NIN-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 20, 2022 | This variant is classified as likely 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