chr9-127509130-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022833.4(NIBAN2):c.1163A>T(p.Tyr388Phe) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,458,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022833.4 missense, splice_region
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 | UniProt |
---|---|---|---|---|---|---|---|
NIBAN2 | NM_022833.4 | c.1163A>T | p.Tyr388Phe | missense_variant, splice_region_variant | 10/14 | ENST00000373312.4 | |
NIBAN2 | NM_001035534.3 | c.1124A>T | p.Tyr375Phe | missense_variant, splice_region_variant | 10/14 | ||
NIBAN2 | XM_005252135.3 | c.1382A>T | p.Tyr461Phe | missense_variant, splice_region_variant | 11/15 | ||
NIBAN2 | XM_011518925.2 | c.1253A>T | p.Tyr418Phe | missense_variant, splice_region_variant | 11/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIBAN2 | ENST00000373312.4 | c.1163A>T | p.Tyr388Phe | missense_variant, splice_region_variant | 10/14 | 1 | NM_022833.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458110Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 725322
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2023 | The c.1163A>T (p.Y388F) alteration is located in exon 10 (coding exon 10) of the FAM129B gene. This alteration results from a A to T substitution at nucleotide position 1163, causing the tyrosine (Y) at amino acid position 388 to be replaced by a phenylalanine (F). 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
Publications
No publications associated with this variant yet.