dbSNP rs3046151: NFIX:c.27+290_27+307delTGTGTGTGTGTGTGTGTG (chr19-12996142-CGTGTGTGTGTGTGTGTGT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001365902.3(NFIX):c.27+290_27+307delTGTGTGTGTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

NFIX
NM_001365902.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Variant links:

Genes affected

NFIX (HGNC:7788): (nuclear factor I X) The protein encoded by this gene is a transcription factor that binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3 in viral and cellular promoters. The encoded protein can also stimulate adenovirus replication in vitro. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]

NFIX links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3 link	c.27+290_27+307delTGTGTGTGTGTGTGTGTG	intron_variant	Intron 1 of 10	ENST00000592199.6	NP_001352831.1
NFIX	NM_002501.4 link	c.27+290_27+307delTGTGTGTGTGTGTGTGTG	intron_variant	Intron 1 of 9		NP_002492.2	Q14938-3
NFIX	NM_001365982.2 link	c.27+290_27+307delTGTGTGTGTGTGTGTGTG	intron_variant	Intron 1 of 8		NP_001352911.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIX	ENST00000592199.6 link	c.27+279_27+296delGTGTGTGTGTGTGTGTGT		intron_variant	Intron 1 of 10	5	NM_001365902.3	ENSP00000467512.1		Q14938-1
NFIX	ENST00000397661.6 link	c.27+279_27+296delGTGTGTGTGTGTGTGTGT		intron_variant	Intron 1 of 9	5		ENSP00000380781.2		Q14938-3

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.