chr7-144397625-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001080413.3(NOBOX):c.1775-84G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,210,516 control chromosomes in the GnomAD database, including 154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.011 ( 13 hom., cov: 32)
Exomes 𝑓: 0.015 ( 141 hom. )
Consequence
NOBOX
NM_001080413.3 intron
NM_001080413.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.487
Publications
2 publications found
Genes affected
NOBOX (HGNC:22448): (NOBOX oogenesis homeobox) This homeobox gene encodes a transcription factor that is thought to play a role in oogenesis. In mice, it is essential for folliculogenesis and regulation of oocyte-specific genes. Defects in this gene result in premature ovarian failure type 5.[provided by RefSeq, May 2011]
NOBOX Gene-Disease associations (from GenCC):
- premature ovarian failure 5Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 7-144397625-C-T is Benign according to our data. Variant chr7-144397625-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1201840.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.011 (1673/152284) while in subpopulation NFE AF = 0.0168 (1145/68018). AF 95% confidence interval is 0.016. There are 13 homozygotes in GnomAd4. There are 788 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAd4 at 1673 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOBOX | NM_001080413.3 | c.1775-84G>A | intron_variant | Intron 9 of 9 | ENST00000467773.1 | NP_001073882.3 | ||
NOBOX | NM_001436401.1 | c.1424-84G>A | intron_variant | Intron 7 of 7 | NP_001423330.1 | |||
NOBOX | NM_001436402.1 | c.872-84G>A | intron_variant | Intron 6 of 6 | NP_001423331.1 | |||
NOBOX | XM_017011742.3 | c.1679-84G>A | intron_variant | Intron 9 of 9 | XP_016867231.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOBOX | ENST00000467773.1 | c.1775-84G>A | intron_variant | Intron 9 of 9 | 5 | NM_001080413.3 | ENSP00000419457.1 | |||
NOBOX | ENST00000483238.5 | c.1679-84G>A | intron_variant | Intron 9 of 9 | 5 | ENSP00000419565.1 | ||||
NOBOX | ENST00000645489.1 | c.1424-84G>A | intron_variant | Intron 7 of 7 | ENSP00000496732.1 | |||||
NOBOX | ENST00000643164.1 | c.872-84G>A | intron_variant | Intron 6 of 6 | ENSP00000495343.1 |
Frequencies
GnomAD3 genomes AF: 0.0110 AC: 1676AN: 152166Hom.: 13 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1676
AN:
152166
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0154 AC: 16317AN: 1058232Hom.: 141 AF XY: 0.0150 AC XY: 7832AN XY: 521720 show subpopulations
GnomAD4 exome
AF:
AC:
16317
AN:
1058232
Hom.:
AF XY:
AC XY:
7832
AN XY:
521720
show subpopulations
African (AFR)
AF:
AC:
62
AN:
24198
American (AMR)
AF:
AC:
213
AN:
21482
Ashkenazi Jewish (ASJ)
AF:
AC:
391
AN:
17726
East Asian (EAS)
AF:
AC:
2
AN:
33846
South Asian (SAS)
AF:
AC:
564
AN:
57896
European-Finnish (FIN)
AF:
AC:
260
AN:
30542
Middle Eastern (MID)
AF:
AC:
83
AN:
3476
European-Non Finnish (NFE)
AF:
AC:
14070
AN:
823164
Other (OTH)
AF:
AC:
672
AN:
45902
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
801
1601
2402
3202
4003
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0110 AC: 1673AN: 152284Hom.: 13 Cov.: 32 AF XY: 0.0106 AC XY: 788AN XY: 74452 show subpopulations
GnomAD4 genome
AF:
AC:
1673
AN:
152284
Hom.:
Cov.:
32
AF XY:
AC XY:
788
AN XY:
74452
show subpopulations
African (AFR)
AF:
AC:
140
AN:
41566
American (AMR)
AF:
AC:
104
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
80
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5172
South Asian (SAS)
AF:
AC:
29
AN:
4824
European-Finnish (FIN)
AF:
AC:
119
AN:
10616
Middle Eastern (MID)
AF:
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1145
AN:
68018
Other (OTH)
AF:
AC:
21
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
89
178
267
356
445
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
May 20, 2019
GeneDx
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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