3-101853587-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_031419.4(NFKBIZ):c.1061C>G(p.Ala354Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFKBIZ | NM_031419.4 | c.1061C>G | p.Ala354Gly | missense_variant | 5/12 | ENST00000326172.9 | |
NFKBIZ | NM_001005474.3 | c.761C>G | p.Ala254Gly | missense_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIZ | ENST00000326172.9 | c.1061C>G | p.Ala354Gly | missense_variant | 5/12 | 1 | NM_031419.4 | P4 | |
NFKBIZ | ENST00000394054.6 | c.761C>G | p.Ala254Gly | missense_variant | 6/13 | 1 | A2 | ||
NFKBIZ | ENST00000483180.5 | c.761C>G | p.Ala254Gly | missense_variant | 5/11 | 5 | |||
NFKBIZ | ENST00000326151.9 | c.709-14C>G | splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251492Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135920
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 727248
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 27, 2022 | The c.1061C>G (p.A354G) alteration is located in exon 5 (coding exon 5) of the NFKBIZ gene. This alteration results from a C to G substitution at nucleotide position 1061, causing the alanine (A) at amino acid position 354 to be replaced by a glycine (G). 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