chr6-31547563-T-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001144962.2(NFKBIL1):c.-13+590T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 558,646 control chromosomes in the GnomAD database, including 33,185 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.37 ( 10718 hom., cov: 29)
Exomes 𝑓: 0.33 ( 22467 hom. )
Consequence
NFKBIL1
NM_001144962.2 intron
NM_001144962.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.27
Genes affected
NFKBIL1 (HGNC:7800): (NFKB inhibitor like 1) This gene encodes a divergent member of the I-kappa-B family of proteins. Its function has not been determined. The gene lies within the major histocompatibility complex (MHC) class I region on chromosome 6. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2009]
ATP6V1G2 (HGNC:862): (ATPase H+ transporting V1 subunit G2) This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c'', and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This encoded protein is one of three V1 domain G subunit proteins. This gene had previous gene symbols of ATP6G and ATP6G2. Alternatively spliced transcript variants encoding different isoforms have been described. Read-through transcription also exists between this gene and the downstream DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B) gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFKBIL1 | NM_001144962.2 | c.-13+590T>A | intron_variant | NP_001138434.1 | ||||
NFKBIL1 | NM_001144963.2 | c.-13+590T>A | intron_variant | NP_001138435.1 | ||||
NFKBIL1 | NM_005007.4 | upstream_gene_variant | ENST00000376148.9 | NP_004998.3 | ||||
NFKBIL1 | NM_001144961.2 | upstream_gene_variant | NP_001138433.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFKBIL1 | ENST00000376146.8 | c.-13+590T>A | intron_variant | 4 | ENSP00000365316 | A1 | ||||
ATP6V1G2 | ENST00000415099.2 | c.202+663A>T | intron_variant | 5 | ENSP00000390148 | |||||
NFKBIL1 | ENST00000376148.9 | upstream_gene_variant | 1 | NM_005007.4 | ENSP00000365318 | P4 | ||||
NFKBIL1 | ENST00000376145.8 | upstream_gene_variant | 1 | ENSP00000365315 |
Frequencies
GnomAD3 genomes AF: 0.368 AC: 55736AN: 151310Hom.: 10707 Cov.: 29
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GnomAD4 exome AF: 0.325 AC: 132403AN: 407214Hom.: 22467 Cov.: 5 AF XY: 0.322 AC XY: 69261AN XY: 214892
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GnomAD4 genome AF: 0.368 AC: 55784AN: 151432Hom.: 10718 Cov.: 29 AF XY: 0.365 AC XY: 26993AN XY: 73978
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Rheumatoid arthritis Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Feb 01, 2003 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at