chr7-144398297-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001080413.3(NOBOX):c.1759C>T(p.Pro587Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,537,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080413.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOBOX | NM_001080413.3 | c.1759C>T | p.Pro587Ser | missense_variant | 9/10 | ENST00000467773.1 | |
NOBOX | XM_017011742.3 | c.1663C>T | p.Pro555Ser | missense_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOBOX | ENST00000467773.1 | c.1759C>T | p.Pro587Ser | missense_variant | 9/10 | 5 | NM_001080413.3 | ||
NOBOX | ENST00000483238.5 | c.1663C>T | p.Pro555Ser | missense_variant | 9/10 | 5 | A2 | ||
NOBOX | ENST00000645489.1 | c.1408C>T | p.Pro470Ser | missense_variant | 7/8 | P2 | |||
NOBOX | ENST00000643164.1 | c.856C>T | p.Pro286Ser | missense_variant | 6/7 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000351 AC: 5AN: 142254Hom.: 0 AF XY: 0.0000394 AC XY: 3AN XY: 76122
GnomAD4 exome AF: 0.0000231 AC: 32AN: 1384964Hom.: 0 Cov.: 32 AF XY: 0.0000219 AC XY: 15AN XY: 683426
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74330
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.1759C>T (p.P587S) alteration is located in exon 9 (coding exon 9) of the NOBOX gene. This alteration results from a C to T substitution at nucleotide position 1759, causing the proline (P) at amino acid position 587 to be replaced by a serine (S). 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