rs2164983

Positions:

• chr19-8679120-C-A
• chr19-8679120-C-G

Variant summary

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

The NM_001378600.1(NFILZ):​c.*1485C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,570 control chromosomes in the GnomAD database, including 2,909 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 0.19 (2909 hom., cov: 30)
• Consequence: NFILZ NM_001378600.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFILZ	NM_001378600.1	c.*1485C>A		3_prime_UTR_variant	6/6	ENST00000691075.1
NFILZ	NM_001378599.1	c.*1485C>A		3_prime_UTR_variant	7/7
NFILZ	NM_001378601.1	c.*1485C>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFILZ	ENST00000691075.1	c.*1485C>A		3_prime_UTR_variant	6/6		NM_001378600.1	P1
NFILZ	ENST00000570582.4	c.*1485C>A		3_prime_UTR_variant	4/4			P1
NFILZ	ENST00000671902.2	c.*1485C>A		3_prime_UTR_variant	6/6			P1
NFILZ	ENST00000673603.2	c.*1485C>A		3_prime_UTR_variant	7/7			P1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28580 AN: 151454 Hom.: 2906 Cov.: 30

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.189 AC: 28591 AN: 151570 Hom.: 2909 Cov.: 30 AF XY: 0.191 AC XY: 14110 AN XY: 74052

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.180

Alfa AF: 0.147 Hom.: 1437

Bravo AF: 0.196

Asia WGS AF: 0.117 AC: 406 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.5
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: rs2164983; hg19: chr19-8789381;