NR_188612.1:n.2072G>A

Variant names:

• chr9-91426104-G-A
• rs813498
• NR_188612.1:n.2072G>A

Variant summary

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

The NR_188612.1(LOC105376146):​n.2072G>A variant causes a non coding transcript exon 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: LOC105376146 NR_188612.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 5 publications found

Genes affected

LOC105376146 (HGNC:):

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=-0.85).
• 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 rank	MANE	Protein	UniProt
LOC105376146	NR_188612.1	n.2072G>A		non_coding_transcript_exon_variant	Exon 1 of 2
NFIL3	XM_047423425.1	c.-172-15198C>T		intron_variant	Intron 1 of 1		XP_047279381.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233081	ENST00000832485.1	n.340-726G>A		intron_variant	Intron 1 of 1
ENSG00000233081	ENST00000832486.1	n.151-726G>A		intron_variant	Intron 1 of 1
ENSG00000233081	ENST00000832487.1	n.741-726G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.987 AC: 41030 AN: 41554

American (AMR) AF: 0.965 AC: 14770 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3237 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5179 AN: 5180

South Asian (SAS) AF: 0.994 AC: 4795 AN: 4826

European-Finnish (FIN) AF: 0.990 AC: 10506 AN: 10614

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65089 AN: 68040

Other (OTH) AF: 0.952 AC: 2012 AN: 2114

Alfa AF: 0.961 Hom.: 76283

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
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs813498; hg19: chr9-94188386;