chr7-144397368-C-T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080413.3(NOBOX):βc.1948G>Aβ(p.Glu650Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000325 in 1,537,174 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 (β ).
Frequency
Consequence
NM_001080413.3 missense
Scores
Clinical Significance
Conservation
Publications
- premature ovarian failure 5Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOBOX | NM_001080413.3 | c.1948G>A | p.Glu650Lys | missense_variant | Exon 10 of 10 | ENST00000467773.1 | NP_001073882.3 | |
NOBOX | NM_001436401.1 | c.1597G>A | p.Glu533Lys | missense_variant | Exon 8 of 8 | NP_001423330.1 | ||
NOBOX | NM_001436402.1 | c.1045G>A | p.Glu349Lys | missense_variant | Exon 7 of 7 | NP_001423331.1 | ||
NOBOX | XM_017011742.3 | c.1852G>A | p.Glu618Lys | missense_variant | Exon 10 of 10 | XP_016867231.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOBOX | ENST00000467773.1 | c.1948G>A | p.Glu650Lys | missense_variant | Exon 10 of 10 | 5 | NM_001080413.3 | ENSP00000419457.1 | ||
NOBOX | ENST00000483238.5 | c.1852G>A | p.Glu618Lys | missense_variant | Exon 10 of 10 | 5 | ENSP00000419565.1 | |||
NOBOX | ENST00000645489.1 | c.1597G>A | p.Glu533Lys | missense_variant | Exon 8 of 8 | ENSP00000496732.1 | ||||
NOBOX | ENST00000643164.1 | c.*143G>A | downstream_gene_variant | ENSP00000495343.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000707 AC: 1AN: 141476 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000289 AC: 4AN: 1384938Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 683394 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372 show subpopulations
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1948G>A (p.E650K) alteration is located in exon 10 (coding exon 10) of the NOBOX gene. This alteration results from a G to A substitution at nucleotide position 1948, causing the glutamic acid (E) at amino acid position 650 to be replaced by a lysine (K). 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