chr9-91451720-T-C

Variant names:

• chr9-91451720-T-C
• rs1412470
• XM_047423425.1:c.-173+31627A>G

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+31627A>G 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 152,022 control chromosomes in the GnomAD database, including 19,316 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 (19316 hom., cov: 32)
• Consequence: NFIL3 XM_047423425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68425 AN: 151904 Hom.: 19266 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: 0.350

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.451 AC: 68528 AN: 152022 Hom.: 19316 Cov.: 32 AF XY: 0.451 AC XY: 33520 AN XY: 74292

African (AFR) AF: 0.791 AC: 32786 AN: 41456

American (AMR) AF: 0.302 AC: 4611 AN: 15282

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

East Asian (EAS) AF: 0.661 AC: 3412 AN: 5162

South Asian (SAS) AF: 0.427 AC: 2060 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3693 AN: 10564

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

European-Non Finnish (NFE) AF: 0.285 AC: 19372 AN: 67954

Other (OTH) AF: 0.434 AC: 914 AN: 2108

Alfa AF: 0.343 Hom.: 31553

Bravo AF: 0.465

Asia WGS AF: 0.577 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1412470; hg19: chr9-94214002; COSMIC: COSV60378006;