rs2164983

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001378600.1(NFILZ):​c.*1485C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,570 control chromosomes in the GnomAD database, including 2,909 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 0.19 ( 2909 hom., cov: 30)

Consequence

NFILZ
NM_001378600.1 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NFILZNM_001378600.1 linkuse as main transcriptc.*1485C>A 3_prime_UTR_variant 6/6 ENST00000691075.1
NFILZNM_001378599.1 linkuse as main transcriptc.*1485C>A 3_prime_UTR_variant 7/7
NFILZNM_001378601.1 linkuse as main transcriptc.*1485C>A 3_prime_UTR_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NFILZENST00000691075.1 linkuse as main transcriptc.*1485C>A 3_prime_UTR_variant 6/6 NM_001378600.1 P1
NFILZENST00000570582.4 linkuse as main transcriptc.*1485C>A 3_prime_UTR_variant 4/4 P1
NFILZENST00000671902.2 linkuse as main transcriptc.*1485C>A 3_prime_UTR_variant 6/6 P1
NFILZENST00000673603.2 linkuse as main transcriptc.*1485C>A 3_prime_UTR_variant 7/7 P1

Frequencies

GnomAD3 genomes
AF:
0.189
AC:
28580
AN:
151454
Hom.:
2906
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.231
Gnomad AMI
AF:
0.215
Gnomad AMR
AF:
0.237
Gnomad ASJ
AF:
0.189
Gnomad EAS
AF:
0.123
Gnomad SAS
AF:
0.103
Gnomad FIN
AF:
0.245
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.155
Gnomad OTH
AF:
0.182
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.189
AC:
28591
AN:
151570
Hom.:
2909
Cov.:
30
AF XY:
0.191
AC XY:
14110
AN XY:
74052
show subpopulations
Gnomad4 AFR
AF:
0.231
Gnomad4 AMR
AF:
0.237
Gnomad4 ASJ
AF:
0.189
Gnomad4 EAS
AF:
0.122
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.245
Gnomad4 NFE
AF:
0.155
Gnomad4 OTH
AF:
0.180
Alfa
AF:
0.147
Hom.:
1437
Bravo
AF:
0.196
Asia WGS
AF:
0.117
AC:
406
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
4.5
DANN
Benign
0.81

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2164983; hg19: chr19-8789381; API