chr12-663507-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000543884.2(NINJ2-AS1):n.400C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000885 in 1,582,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000543884.2 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NINJ2-AS1 | ENST00000543884.2 | n.400C>T | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
NINJ2 | ENST00000662884.1 | c.-9G>A | 5_prime_UTR_variant | 1/4 | |||||
NINJ2-AS1 | ENST00000662519.1 | n.643C>T | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000889 AC: 2AN: 224972Hom.: 0 AF XY: 0.0000165 AC XY: 2AN XY: 120972
GnomAD4 exome AF: 0.00000699 AC: 10AN: 1430426Hom.: 0 Cov.: 35 AF XY: 0.00000705 AC XY: 5AN XY: 709102
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152042Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74252
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at