NM_001378600.1:c.-163-854A>C

Variant names:

• chr19-8673697-A-C
• rs2967682
• NM_001378600.1:c.-163-854A>C

Variant summary

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

The NM_001378600.1(NFILZ):​c.-163-854A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,820 control chromosomes in the GnomAD database, including 38,368 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 0.70 (38368 hom., cov: 31)
• Consequence: NFILZ NM_001378600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 6 publications found

Genes affected

NFILZ (HGNC:52681): (NFIL3 like basic leucine zipper) Predicted to enable DNA binding activity and DNA-binding transcription factor activity. Predicted to be involved in immune response; regulation of transcription, DNA-templated; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378600.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFILZ	NM_001378600.1	MANE Select	c.-163-854A>C		intron	N/A	NP_001365529.1
	NFILZ	NM_001378599.1		c.-163-854A>C		intron	N/A	NP_001365528.1
	NFILZ	NM_001378601.1		c.-65-854A>C		intron	N/A	NP_001365530.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFILZ	ENST00000691075.1	MANE Select	c.-163-854A>C		intron	N/A	ENSP00000509575.1
	NFILZ	ENST00000570582.4	TSL:6	c.-157-854A>C		intron	N/A	ENSP00000500121.1
	NFILZ	ENST00000671902.2		c.-161-854A>C		intron	N/A	ENSP00000500604.1

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106139 AN: 151702 Hom.: 38317 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.700 AC: 106246 AN: 151820 Hom.: 38368 Cov.: 31 AF XY: 0.704 AC XY: 52235 AN XY: 74180

African (AFR) AF: 0.871 AC: 36058 AN: 41414

American (AMR) AF: 0.712 AC: 10867 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2236 AN: 3460

East Asian (EAS) AF: 0.859 AC: 4442 AN: 5172

South Asian (SAS) AF: 0.787 AC: 3794 AN: 4818

European-Finnish (FIN) AF: 0.647 AC: 6819 AN: 10536

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40005 AN: 67858

Other (OTH) AF: 0.663 AC: 1396 AN: 2104

Alfa AF: 0.629 Hom.: 91258

Bravo AF: 0.712

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2967682; hg19: chr19-8783532;