chr12-663365-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016533.6(NINJ2):c.-5G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016533.6 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NINJ2 | NM_016533.6 | c.-5G>A | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000305108.10 | NP_057617.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NINJ2 | ENST00000305108.10 | c.-5G>A | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_016533.6 | ENSP00000307552.5 | |||
NINJ2 | ENST00000662884.1 | c.134G>A | p.Ser45Asn | missense_variant | Exon 1 of 4 | ENSP00000499548.1 | ||||
NINJ2-AS1 | ENST00000543884.2 | n.258C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
NINJ2-AS1 | ENST00000662519.1 | n.501C>T | non_coding_transcript_exon_variant | Exon 3 of 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251116Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135738
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727232
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.134G>A (p.S45N) alteration is located in exon 1 (coding exon 1) of the NINJ2 gene. This alteration results from a G to A substitution at nucleotide position 134, causing the serine (S) at amino acid position 45 to be replaced by an asparagine (N). 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