chr9-91425859-G-A

Position:

• chr9-91425859-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047423425.1(NFIL3):​c.-172-14953C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0566 in 152,268 control chromosomes in the GnomAD database, including 311 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 0.057 (311 hom., cov: 33)
• Consequence: NFIL3 XM_047423425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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]

LOC105376146 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIL3	XM_047423425.1	c.-172-14953C>T		intron_variant			XP_047279381.1
LOC105376146	NR_188612.1	n.1827G>A		non_coding_transcript_exon_variant	1/2
		n.91425859G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 8629 AN: 152150 Hom.: 313 Cov.: 33

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0566 AC: 8624 AN: 152268 Hom.: 311 Cov.: 33 AF XY: 0.0572 AC XY: 4257 AN XY: 74448

Gnomad4 AFR AF: 0.0260

Gnomad4 AMR AF: 0.0519

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0636

Gnomad4 SAS AF: 0.0593

Gnomad4 FIN AF: 0.0673

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0699

Alfa AF: 0.0707 Hom.: 530

Bravo AF: 0.0540

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13297268; hg19: chr9-94188141;