chr6-31557745-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005007.4(NFKBIL1):c.452C>T(p.Ala151Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.452C>T | p.Ala151Val | missense_variant | 3/4 | ENST00000376148.9 | NP_004998.3 | |
NFKBIL1 | NM_001144961.2 | c.452C>T | p.Ala151Val | missense_variant | 3/4 | NP_001138433.1 | ||
NFKBIL1 | NM_001144962.2 | c.383C>T | p.Ala128Val | missense_variant | 3/4 | NP_001138434.1 | ||
NFKBIL1 | NM_001144963.2 | c.383C>T | p.Ala128Val | missense_variant | 3/4 | NP_001138435.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFKBIL1 | ENST00000376148.9 | c.452C>T | p.Ala151Val | missense_variant | 3/4 | 1 | NM_005007.4 | ENSP00000365318 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250368Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135356
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460214Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726172
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152218Hom.: 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 | Jan 03, 2024 | The c.452C>T (p.A151V) alteration is located in exon 3 (coding exon 3) of the NFKBIL1 gene. This alteration results from a C to T substitution at nucleotide position 452, causing the alanine (A) at amino acid position 151 to be replaced by a valine (V). 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