chr3-101849803-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031419.4(NFKBIZ):c.175G>A(p.Ala59Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000034 in 1,470,126 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031419.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIZ | NM_031419.4 | c.175G>A | p.Ala59Thr | missense_variant | 1/12 | ENST00000326172.9 | |
NFKBIZ | NM_001005474.3 | c.-11-2282G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIZ | ENST00000326172.9 | c.175G>A | p.Ala59Thr | missense_variant | 1/12 | 1 | NM_031419.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151848Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000136 AC: 1AN: 73500Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 42630
GnomAD4 exome AF: 0.00000228 AC: 3AN: 1318278Hom.: 0 Cov.: 31 AF XY: 0.00000154 AC XY: 1AN XY: 650406
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151848Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74162
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.175G>A (p.A59T) alteration is located in exon 1 (coding exon 1) of the NFKBIZ gene. This alteration results from a G to A substitution at nucleotide position 175, causing the alanine (A) at amino acid position 59 to be replaced by a threonine (T). 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