6-31557759-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005007.4(NFKBIL1):āc.466G>Cā(p.Glu156Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,588 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005007.4 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFKBIL1 | NM_005007.4 | c.466G>C | p.Glu156Gln | missense_variant | 3/4 | ENST00000376148.9 | NP_004998.3 | |
NFKBIL1 | NM_001144961.2 | c.466G>C | p.Glu156Gln | missense_variant | 3/4 | NP_001138433.1 | ||
NFKBIL1 | NM_001144962.2 | c.397G>C | p.Glu133Gln | missense_variant | 3/4 | NP_001138434.1 | ||
NFKBIL1 | NM_001144963.2 | c.397G>C | p.Glu133Gln | missense_variant | 3/4 | NP_001138435.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFKBIL1 | ENST00000376148.9 | c.466G>C | p.Glu156Gln | missense_variant | 3/4 | 1 | NM_005007.4 | ENSP00000365318 | P4 | |
NFKBIL1 | ENST00000376145.8 | c.466G>C | p.Glu156Gln | missense_variant | 3/4 | 1 | ENSP00000365315 | |||
NFKBIL1 | ENST00000376146.8 | c.397G>C | p.Glu133Gln | missense_variant | 3/4 | 4 | ENSP00000365316 | A1 | ||
NFKBIL1 | ENST00000473655.1 | n.500G>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 152238Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460588Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726406
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.466G>C (p.E156Q) alteration is located in exon 3 (coding exon 3) of the NFKBIL1 gene. This alteration results from a G to C substitution at nucleotide position 466, causing the glutamic acid (E) at amino acid position 156 to be replaced by a glutamine (Q). 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