chr5-93593851-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005654.6(NR2F1):c.*9C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,611,164 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 2 hom. )
Consequence
NR2F1
NM_005654.6 3_prime_UTR
NM_005654.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.48
Publications
1 publications found
Genes affected
NR2F1 (HGNC:7975): (nuclear receptor subfamily 2 group F member 1) The protein encoded by this gene is a nuclear hormone receptor and transcriptional regulator. The encoded protein acts as a homodimer and binds to 5'-AGGTCA-3' repeats. Defects in this gene are a cause of Bosch-Boonstra optic atrophy syndrome (BBOAS). [provided by RefSeq, Apr 2014]
NR2F1 Gene-Disease associations (from GenCC):
- Bosch-Boonstra-Schaaf optic atrophy syndromeInheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, ClinGen, Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BS1
Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0000854 (13/152278) while in subpopulation SAS AF = 0.00124 (6/4826). AF 95% confidence interval is 0.000541. There are 0 homozygotes in GnomAd4. There are 7 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAdExome4 at 2 AD,AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152160Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
14
AN:
152160
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:
GnomAD2 exomes AF: 0.000196 AC: 49AN: 249734 AF XY: 0.000222 show subpopulations
GnomAD2 exomes
AF:
AC:
49
AN:
249734
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000134 AC: 195AN: 1458886Hom.: 2 Cov.: 31 AF XY: 0.000165 AC XY: 120AN XY: 725280 show subpopulations
GnomAD4 exome
AF:
AC:
195
AN:
1458886
Hom.:
Cov.:
31
AF XY:
AC XY:
120
AN XY:
725280
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33428
American (AMR)
AF:
AC:
9
AN:
44638
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25944
East Asian (EAS)
AF:
AC:
0
AN:
39652
South Asian (SAS)
AF:
AC:
115
AN:
86040
European-Finnish (FIN)
AF:
AC:
1
AN:
53288
Middle Eastern (MID)
AF:
AC:
9
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
55
AN:
1109888
Other (OTH)
AF:
AC:
6
AN:
60252
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
11
22
32
43
54
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74450 show subpopulations
GnomAD4 genome
AF:
AC:
13
AN:
152278
Hom.:
Cov.:
32
AF XY:
AC XY:
7
AN XY:
74450
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41556
American (AMR)
AF:
AC:
1
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5184
South Asian (SAS)
AF:
AC:
6
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10602
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
4
AN:
68024
Other (OTH)
AF:
AC:
1
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.514
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Jun 07, 2018
Athena Diagnostics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Apr 10, 2020
GeneDx
Significance: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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