4-139043115-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_012118.4(NOCT):c.232C>T(p.Leu78Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,613,350 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_012118.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOCT | ENST00000280614.4 | c.232C>T | p.Leu78Phe | missense_variant | Exon 2 of 3 | 1 | NM_012118.4 | ENSP00000280614.2 | ||
NOCT | ENST00000515616.1 | n.44C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
NOCT | ENST00000630479.1 | n.232C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 5 | ENSP00000486546.1 | ||||
ELF2 | ENST00000515489.1 | n.273-14766G>A | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251230Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135782
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461328Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 726868
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74240
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.232C>T (p.L78F) alteration is located in exon 2 (coding exon 2) of the NOCT gene. This alteration results from a C to T substitution at nucleotide position 232, causing the leucine (L) at amino acid position 78 to be replaced by a phenylalanine (F). 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