chr6-44265498-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000275015.9(NFKBIE):c.266C>T(p.Ala89Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000819 in 1,538,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000275015.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIE | NM_004556.3 | c.-152C>T | 5_prime_UTR_variant | 1/6 | ENST00000619360.6 | ||
POLR1C | NM_001318876.2 | c.946-176392G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIE | ENST00000275015.9 | c.266C>T | p.Ala89Val | missense_variant | 1/6 | 1 | |||
NFKBIE | ENST00000619360.6 | c.-152C>T | 5_prime_UTR_variant | 1/6 | 1 | NM_004556.3 | P1 | ||
NFKBIE | ENST00000477930.2 | c.-152C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 15AN: 133824Hom.: 0 AF XY: 0.000122 AC XY: 9AN XY: 73610
GnomAD4 exome AF: 0.0000822 AC: 114AN: 1386086Hom.: 0 Cov.: 33 AF XY: 0.000105 AC XY: 72AN XY: 683832
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.266C>T (p.A89V) alteration is located in exon 1 (coding exon 1) of the NFKBIE gene. This alteration results from a C to T substitution at nucleotide position 266, causing the alanine (A) at amino acid position 89 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