19-12996142-CGTGT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001365902.3(NFIX):c.27+304_27+307del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.045 (440 hom., cov: 0)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.02

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 Benign. Variant got -10 ACMG points.

• BP6: Variant 19-12996142-CGTGT-C is Benign according to our data. Variant chr19-12996142-CGTGT-C is described in ClinVar as [Benign]. Clinvar id is 1227698.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIX	NM_001365902.3	c.27+304_27+307del		intron_variant		ENST00000592199.6
NFIX	NM_001365982.2	c.27+304_27+307del		intron_variant
NFIX	NM_002501.4	c.27+304_27+307del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIX	ENST00000592199.6	c.27+304_27+307del		intron_variant		5	NM_001365902.3	P4
NFIX	ENST00000397661.6	c.27+304_27+307del		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0449 AC: 6527 AN: 145516 Hom.: 441 Cov.: 0

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.00545

Gnomad FIN AF: 0.00327

Gnomad MID AF: 0.0101

Gnomad NFE AF: 0.00410

Gnomad OTH AF: 0.0323

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

GnomAD4 genome AF: 0.0448 AC: 6523 AN: 145572 Hom.: 440 Cov.: 0 AF XY: 0.0439 AC XY: 3106 AN XY: 70714

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.00547

Gnomad4 FIN AF: 0.00327

Gnomad4 NFE AF: 0.00410

Gnomad4 OTH AF: 0.0319

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 18, 2020

- -

Computational scores

Source: dbNSFP v4.3

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: rs3046151; hg19: chr19-13106956;