6-31557671-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1
The NM_005007.4(NFKBIL1):c.378C>T(p.Ser126=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,575,870 control chromosomes in the GnomAD database, including 19,538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.13 ( 1585 hom., cov: 32)
Exomes 𝑓: 0.15 ( 17953 hom. )
Consequence
NFKBIL1
NM_005007.4 synonymous
NM_005007.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.723
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]
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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=-0.44).
BP6
Variant 6-31557671-C-T is Benign according to our data. Variant chr6-31557671-C-T is described in ClinVar as [Benign]. Clinvar id is 3060308.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.723 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFKBIL1 | NM_005007.4 | c.378C>T | p.Ser126= | synonymous_variant | 3/4 | ENST00000376148.9 | NP_004998.3 | |
NFKBIL1 | NM_001144961.2 | c.378C>T | p.Ser126= | synonymous_variant | 3/4 | NP_001138433.1 | ||
NFKBIL1 | NM_001144962.2 | c.309C>T | p.Ser103= | synonymous_variant | 3/4 | NP_001138434.1 | ||
NFKBIL1 | NM_001144963.2 | c.309C>T | p.Ser103= | synonymous_variant | 3/4 | NP_001138435.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFKBIL1 | ENST00000376148.9 | c.378C>T | p.Ser126= | synonymous_variant | 3/4 | 1 | NM_005007.4 | ENSP00000365318 | P4 |
Frequencies
GnomAD3 genomes AF: 0.132 AC: 20002AN: 151982Hom.: 1587 Cov.: 32
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GnomAD3 exomes AF: 0.163 AC: 38474AN: 236606Hom.: 3369 AF XY: 0.169 AC XY: 21639AN XY: 128228
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GnomAD4 exome AF: 0.154 AC: 218556AN: 1423770Hom.: 17953 Cov.: 33 AF XY: 0.157 AC XY: 110221AN XY: 702874
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GnomAD4 genome AF: 0.132 AC: 20012AN: 152100Hom.: 1585 Cov.: 32 AF XY: 0.136 AC XY: 10083AN XY: 74354
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
NFKBIL1-related disorder Benign:1
Benign, no assertion criteria provided | 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at