4-139045099-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012118.4(NOCT):c.921C>A(p.Asn307Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,614,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOCT | ENST00000280614.4 | c.921C>A | p.Asn307Lys | missense_variant | Exon 3 of 3 | 1 | NM_012118.4 | ENSP00000280614.2 | ||
NOCT | ENST00000515616.1 | n.733C>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 | |||||
ELF2 | ENST00000515489.1 | n.272+15225G>T | intron_variant | Intron 1 of 1 | 2 | |||||
NOCT | ENST00000630479.1 | n.*505-463C>A | intron_variant | Intron 2 of 2 | 5 | ENSP00000486546.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250348Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135274
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461886Hom.: 0 Cov.: 34 AF XY: 0.0000495 AC XY: 36AN XY: 727240
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.921C>A (p.N307K) alteration is located in exon 3 (coding exon 3) of the NOCT gene. This alteration results from a C to A substitution at nucleotide position 921, causing the asparagine (N) at amino acid position 307 to be replaced by a lysine (K). 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