GeneBe

chr19-8679120-C-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001378600.1(NFILZ):​c.*1485C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,802 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 30)

Consequence

NFILZ
NM_001378600.1 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

Publications

34 publications found
Variant links:
Genes affected
NFILZ (HGNC:52681): (NFIL3 like basic leucine zipper) Predicted to enable DNA binding activity and DNA-binding transcription factor activity. Predicted to be involved in immune response; regulation of transcription, DNA-templated; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NFILZNM_001378600.1 linkc.*1485C>G 3_prime_UTR_variant Exon 6 of 6 ENST00000691075.1 NP_001365529.1
NFILZNM_001378599.1 linkc.*1485C>G 3_prime_UTR_variant Exon 7 of 7 NP_001365528.1
NFILZNM_001378601.1 linkc.*1485C>G 3_prime_UTR_variant Exon 3 of 3 NP_001365530.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NFILZENST00000691075.1 linkc.*1485C>G 3_prime_UTR_variant Exon 6 of 6 NM_001378600.1 ENSP00000509575.1 A0A5F9ZHS7
NFILZENST00000570582.4 linkc.*1485C>G 3_prime_UTR_variant Exon 4 of 4 6 ENSP00000500121.1 A0A5F9ZHS7
NFILZENST00000671902.2 linkc.*1485C>G 3_prime_UTR_variant Exon 6 of 6 ENSP00000500604.1 A0A5F9ZHS7
NFILZENST00000673603.2 linkc.*1485C>G 3_prime_UTR_variant Exon 7 of 7 ENSP00000499970.1 A0A5F9ZHS7

Frequencies

GnomAD3 genomes
AF:
0.0000132
AC:
2
AN:
151686
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000132
AC:
2
AN:
151802
Hom.:
0
Cov.:
30
AF XY:
0.0000270
AC XY:
2
AN XY:
74182
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41346
American (AMR)
AF:
0.00
AC:
0
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5144
South Asian (SAS)
AF:
0.000415
AC:
2
AN:
4816
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10504
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67958
Other (OTH)
AF:
0.00
AC:
0
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
0
1
1
2
2
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:
0.00
Hom.:
5110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
4.7
DANN
Benign
0.78
PhyloP100
0.13

Splicing

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

Publications

Other links and lift over

dbSNP: rs2164983; hg19: chr19-8789381; API