rs1058993

Variant names:

• chr19-13023687-A-G
• rs1058993
• NM_001365902.3:c.28-1334A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-13023687-A-G
• chr19-13023687-A-T

Variant summary

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

The NM_001365902.3(NFIX):​c.28-1334A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 27)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

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]

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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3	c.28-1334A>G		intron_variant	Intron 1 of 10	ENST00000592199.6	NP_001352831.1
NFIX	NM_002501.4	c.28-1334A>G		intron_variant	Intron 1 of 9		NP_002492.2
NFIX	NM_001365982.2	c.28-1334A>G		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	c.28-1334A>G		intron_variant	Intron 1 of 10	5	NM_001365902.3	ENSP00000467512.1
NFIX	ENST00000397661.6	c.28-1334A>G		intron_variant	Intron 1 of 9	5		ENSP00000380781.2
NFIX	ENST00000590027.1	c.-114-1334A>G		intron_variant	Intron 1 of 1	2		ENSP00000465616.1
NFIX	ENST00000585382.5	n.-114-1334A>G		intron_variant	Intron 1 of 7	5		ENSP00000466605.1

Frequencies

GnomAD3 genomes Cov.: 27

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

GnomAD4 genome Cov.: 27

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1058993; hg19: chr19-13134501;