chr6-31558135-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005007.4(NFKBIL1):c.670C>T(p.Arg224Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.933 in 1,611,914 control chromosomes in the GnomAD database, including 702,866 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005007.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIL1 | NM_005007.4 | c.670C>T | p.Arg224Cys | missense_variant | 4/4 | ENST00000376148.9 | |
NFKBIL1 | NM_001144961.2 | c.625C>T | p.Arg209Cys | missense_variant | 4/4 | ||
NFKBIL1 | NM_001144962.2 | c.601C>T | p.Arg201Cys | missense_variant | 4/4 | ||
NFKBIL1 | NM_001144963.2 | c.556C>T | p.Arg186Cys | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIL1 | ENST00000376148.9 | c.670C>T | p.Arg224Cys | missense_variant | 4/4 | 1 | NM_005007.4 | P4 | |
NFKBIL1 | ENST00000376145.8 | c.625C>T | p.Arg209Cys | missense_variant | 4/4 | 1 | |||
NFKBIL1 | ENST00000376146.8 | c.601C>T | p.Arg201Cys | missense_variant | 4/4 | 4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.954 AC: 145111AN: 152130Hom.: 69294 Cov.: 31
GnomAD3 exomes AF: 0.955 AC: 231948AN: 242782Hom.: 110974 AF XY: 0.956 AC XY: 127023AN XY: 132808
GnomAD4 exome AF: 0.931 AC: 1359001AN: 1459666Hom.: 633509 Cov.: 76 AF XY: 0.934 AC XY: 677948AN XY: 726054
GnomAD4 genome ? AF: 0.954 AC: 145233AN: 152248Hom.: 69357 Cov.: 31 AF XY: 0.955 AC XY: 71064AN XY: 74426
ClinVar
Submissions by phenotype
NFKBIL1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at