9-127507144-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022833.4(NIBAN2):c.1942G>A(p.Asp648Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,453,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_022833.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NIBAN2 | NM_022833.4 | c.1942G>A | p.Asp648Asn | missense_variant | 14/14 | ENST00000373312.4 | NP_073744.2 | |
NIBAN2 | NM_001035534.3 | c.1903G>A | p.Asp635Asn | missense_variant | 14/14 | NP_001030611.1 | ||
NIBAN2 | XM_005252135.3 | c.2161G>A | p.Asp721Asn | missense_variant | 15/15 | XP_005252192.3 | ||
NIBAN2 | XM_011518925.2 | c.2032G>A | p.Asp678Asn | missense_variant | 15/15 | XP_011517227.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NIBAN2 | ENST00000373312.4 | c.1942G>A | p.Asp648Asn | missense_variant | 14/14 | 1 | NM_022833.4 | ENSP00000362409.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000129 AC: 3AN: 232380Hom.: 0 AF XY: 0.0000237 AC XY: 3AN XY: 126584
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1453328Hom.: 0 Cov.: 31 AF XY: 0.00000277 AC XY: 2AN XY: 722430
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2024 | The c.1942G>A (p.D648N) alteration is located in exon 14 (coding exon 14) of the FAM129B gene. This alteration results from a G to A substitution at nucleotide position 1942, causing the aspartic acid (D) at amino acid position 648 to be replaced by an asparagine (N). 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