rs813498

Positions:

• chr9-91426104-G-A
• chr9-91426104-G-C

Variant summary

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

The XM_047423425.1(NFIL3):​c.-172-15198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 152,310 control chromosomes in the GnomAD database, including 71,752 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 0.97 (71752 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: NFIL3 XM_047423425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIL3	XM_047423425.1	c.-172-15198C>T		intron_variant			XP_047279381.1
LOC105376146	NR_188612.1	n.2072G>A		non_coding_transcript_exon_variant	1/2
		n.91426104G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147679 AN: 152192 Hom.: 71693 Cov.: 32

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.970 AC: 147796 AN: 152310 Hom.: 71752 Cov.: 32 AF XY: 0.973 AC XY: 72470 AN XY: 74472

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.965

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.952

Alfa AF: 0.961 Hom.: 53717

Bravo AF: 0.968

Asia WGS AF: 0.992 AC: 3452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.84
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs813498; hg19: chr9-94188386;