chr9-127507414-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022833.4(NIBAN2):āc.1672G>Cā(p.Val558Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000529 in 1,512,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 32)
Exomes š: 0.0000029 ( 0 hom. )
Consequence
NIBAN2
NM_022833.4 missense
NM_022833.4 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 3.27
Genes affected
NIBAN2 (HGNC:25282): (niban apoptosis regulator 2) Enables transcription coactivator activity. Involved in several processes, including gonadotropin secretion; positive regulation of transcription regulatory region DNA binding activity; and regulation of cellular macromolecule biosynthetic process. Located in several cellular components, including adherens junction; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21035501).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIBAN2 | NM_022833.4 | c.1672G>C | p.Val558Leu | missense_variant | 14/14 | ENST00000373312.4 | |
NIBAN2 | NM_001035534.3 | c.1633G>C | p.Val545Leu | missense_variant | 14/14 | ||
NIBAN2 | XM_005252135.3 | c.1891G>C | p.Val631Leu | missense_variant | 15/15 | ||
NIBAN2 | XM_011518925.2 | c.1762G>C | p.Val588Leu | missense_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIBAN2 | ENST00000373312.4 | c.1672G>C | p.Val558Leu | missense_variant | 14/14 | 1 | NM_022833.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000614 AC: 1AN: 162858Hom.: 0 AF XY: 0.0000117 AC XY: 1AN XY: 85602
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GnomAD4 exome AF: 0.00000294 AC: 4AN: 1360072Hom.: 0 Cov.: 31 AF XY: 0.00000451 AC XY: 3AN XY: 665018
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74340
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1672G>C (p.V558L) alteration is located in exon 14 (coding exon 14) of the FAM129B gene. This alteration results from a G to C substitution at nucleotide position 1672, causing the valine (V) at amino acid position 558 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Polyphen
P;P
Vest4
MutPred
0.25
.;Loss of methylation at K554 (P = 0.072);
MVP
MPC
0.63
ClinPred
D
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at