GeneBe

XM_047423425.1:c.-172-20753C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047423425.1(NFIL3):​c.-172-20753C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,930 control chromosomes in the GnomAD database, including 28,994 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 0.57 ( 28994 hom., cov: 30)

Consequence

NFIL3
XM_047423425.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.860

Publications

9 publications found
Variant links:
Genes affected
NFIL3 (HGNC:7787): (nuclear factor, interleukin 3 regulated) The protein encoded by this gene is a transcriptional regulator that binds as a homodimer to activating transcription factor (ATF) sites in many cellular and viral promoters. The encoded protein represses PER1 and PER2 expression and therefore plays a role in the regulation of circadian rhythm. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2014]

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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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NFIL3XM_047423425.1 linkc.-172-20753C>T intron_variant Intron 1 of 1 XP_047279381.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.574
AC:
87088
AN:
151812
Hom.:
28995
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.216
Gnomad AMI
AF:
0.876
Gnomad AMR
AF:
0.699
Gnomad ASJ
AF:
0.614
Gnomad EAS
AF:
0.478
Gnomad SAS
AF:
0.573
Gnomad FIN
AF:
0.776
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.732
Gnomad OTH
AF:
0.607
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.573
AC:
87101
AN:
151930
Hom.:
28994
Cov.:
30
AF XY:
0.578
AC XY:
42894
AN XY:
74250
show subpopulations
African (AFR)
AF:
0.216
AC:
8950
AN:
41438
American (AMR)
AF:
0.699
AC:
10665
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
0.614
AC:
2129
AN:
3470
East Asian (EAS)
AF:
0.477
AC:
2461
AN:
5154
South Asian (SAS)
AF:
0.574
AC:
2767
AN:
4820
European-Finnish (FIN)
AF:
0.776
AC:
8189
AN:
10554
Middle Eastern (MID)
AF:
0.517
AC:
152
AN:
294
European-Non Finnish (NFE)
AF:
0.732
AC:
49714
AN:
67926
Other (OTH)
AF:
0.604
AC:
1275
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1473
2945
4418
5890
7363
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
710
1420
2130
2840
3550
<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:
0.664
Hom.:
53049
Bravo
AF:
0.552
Asia WGS
AF:
0.485
AC:
1687
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.5
DANN
Benign
0.39
PhyloP100
0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs774227; hg19: chr9-94193941; API