rs2233434
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004556.3(NFKBIE):āc.164T>Cā(p.Val55Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 1,551,674 control chromosomes in the GnomAD database, including 2,343 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004556.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIE | NM_004556.3 | c.164T>C | p.Val55Ala | missense_variant | 1/6 | ENST00000619360.6 | |
POLR1C | NM_001318876.2 | c.946-176707A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIE | ENST00000619360.6 | c.164T>C | p.Val55Ala | missense_variant | 1/6 | 1 | NM_004556.3 | P1 | |
NFKBIE | ENST00000275015.9 | c.581T>C | p.Val194Ala | missense_variant | 1/6 | 1 | |||
NFKBIE | ENST00000477930.2 | c.164T>C | p.Val55Ala | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0519 AC: 7900AN: 152130Hom.: 276 Cov.: 33
GnomAD3 exomes AF: 0.0493 AC: 7662AN: 155550Hom.: 307 AF XY: 0.0464 AC XY: 3809AN XY: 82142
GnomAD4 exome AF: 0.0460 AC: 64350AN: 1399426Hom.: 2067 Cov.: 33 AF XY: 0.0451 AC XY: 31153AN XY: 690260
GnomAD4 genome ? AF: 0.0520 AC: 7911AN: 152248Hom.: 276 Cov.: 33 AF XY: 0.0531 AC XY: 3952AN XY: 74444
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at