19-8679120-C-G

Position:

• chr19-8679120-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001378600.1(NFILZ):​c.*1485C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,802 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 (0 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFILZ	NM_001378600.1	c.*1485C>G		3_prime_UTR_variant	6/6	ENST00000691075.1	NP_001365529.1
NFILZ	NM_001378599.1	c.*1485C>G		3_prime_UTR_variant	7/7		NP_001365528.1
NFILZ	NM_001378601.1	c.*1485C>G		3_prime_UTR_variant	3/3		NP_001365530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFILZ	ENST00000691075.1	c.*1485C>G		3_prime_UTR_variant	6/6		NM_001378600.1	ENSP00000509575.1
NFILZ	ENST00000570582.4	c.*1485C>G		3_prime_UTR_variant	4/4	6		ENSP00000500121.1
NFILZ	ENST00000671902.2	c.*1485C>G		3_prime_UTR_variant	6/6			ENSP00000500604.1
NFILZ	ENST00000673603.2	c.*1485C>G		3_prime_UTR_variant	7/7			ENSP00000499970.1

Frequencies

GnomAD3 genomes AF: 0.0000132 AC: 2 AN: 151686 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000132 AC: 2 AN: 151802 Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2 AN XY: 74182

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.78

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;