chr9-91447930-C-T

Variant names:

• chr9-91447930-C-T
• rs4744045
• XM_047423425.1:c.-173+35417G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047423425.1(NFIL3):​c.-173+35417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,982 control chromosomes in the GnomAD database, including 19,305 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 0.45 (19305 hom., cov: 32)
• Consequence: NFIL3 XM_047423425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68409 AN: 151864 Hom.: 19255 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.433

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.451 AC: 68512 AN: 151982 Hom.: 19305 Cov.: 32 AF XY: 0.451 AC XY: 33525 AN XY: 74268

African (AFR) AF: 0.790 AC: 32785 AN: 41498

American (AMR) AF: 0.302 AC: 4602 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1309 AN: 3470

East Asian (EAS) AF: 0.662 AC: 3416 AN: 5164

South Asian (SAS) AF: 0.427 AC: 2059 AN: 4822

European-Finnish (FIN) AF: 0.351 AC: 3692 AN: 10518

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19364 AN: 67952

Other (OTH) AF: 0.434 AC: 915 AN: 2106

Alfa AF: 0.353 Hom.: 8614

Bravo AF: 0.465

Asia WGS AF: 0.575 AC: 1997 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4744045; hg19: chr9-94210212; COSMIC: COSV60377947;