1-184795393-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052966.4(NIBAN1):c.2371G>T(p.Val791Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000181 in 1,605,716 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_052966.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIBAN1 | NM_052966.4 | c.2371G>T | p.Val791Leu | missense_variant | 14/14 | ENST00000367511.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIBAN1 | ENST00000367511.4 | c.2371G>T | p.Val791Leu | missense_variant | 14/14 | 1 | NM_052966.4 | P1 | |
NIBAN1 | ENST00000417056.5 | c.260+2686G>T | intron_variant | 3 | |||||
NIBAN1 | ENST00000487074.5 | n.1843G>T | non_coding_transcript_exon_variant | 9/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000577 AC: 14AN: 242616Hom.: 0 AF XY: 0.0000381 AC XY: 5AN XY: 131090
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1453508Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 722504
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.2371G>T (p.V791L) alteration is located in exon 14 (coding exon 14) of the FAM129A gene. This alteration results from a G to T substitution at nucleotide position 2371, causing the valine (V) at amino acid position 791 to be replaced by a leucine (L). 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