3-101853473-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_031419.4(NFKBIZ):c.947C>G(p.Pro316Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,614,206 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.947C>G | p.Pro316Arg | missense_variant | 5/12 | ENST00000326172.9 | |
NFKBIZ | NM_001005474.3 | c.647C>G | p.Pro216Arg | missense_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFKBIZ | ENST00000326172.9 | c.947C>G | p.Pro316Arg | missense_variant | 5/12 | 1 | NM_031419.4 | P4 | |
NFKBIZ | ENST00000394054.6 | c.647C>G | p.Pro216Arg | missense_variant | 6/13 | 1 | A2 | ||
NFKBIZ | ENST00000483180.5 | c.647C>G | p.Pro216Arg | missense_variant | 5/11 | 5 | |||
NFKBIZ | ENST00000326151.9 | c.709-128C>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000440 AC: 67AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251482Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135916
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.0000344 AC XY: 25AN XY: 727248
GnomAD4 genome ? AF: 0.000440 AC: 67AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 05, 2022 | The c.947C>G (p.P316R) 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 947, causing the proline (P) at amino acid position 316 to be replaced by an arginine (R). 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