19-13024113-CA-C

Variant summary

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

The NM_001365902.3(NFIX):c.28-891del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 405,882 control chromosomes in the GnomAD database, including 112 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.046 (109 hom., cov: 28)
  • Exomes 𝑓: 0.16 (3 hom.)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.632

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 19-13024113-CA-C is Benign according to our data. Variant chr19-13024113-CA-C is described in ClinVar as [Benign]. Clinvar id is 1269465.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIX	NM_001365902.3	c.28-891del		intron_variant		ENST00000592199.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIX	ENST00000592199.6	c.28-891del		intron_variant		5	NM_001365902.3	P4

Frequencies

GnomAD3 genomes AF: 0.0460 AC: 4719 AN: 102590 Hom.: 109 Cov.: 28

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0258

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0394

GnomAD4 exome AF: 0.156 AC: 47449 AN: 303288 Hom.: 3 AF XY: 0.157 AC XY: 25600 AN XY: 163522

Gnomad4 AFR exome AF: 0.175

Gnomad4 AMR exome AF: 0.158

Gnomad4 ASJ exome AF: 0.203

Gnomad4 EAS exome AF: 0.158

Gnomad4 SAS exome AF: 0.139

Gnomad4 FIN exome AF: 0.155

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.163

GnomAD4 genome AF: 0.0460 AC: 4723 AN: 102594 Hom.: 109 Cov.: 28 AF XY: 0.0473 AC XY: 2314 AN XY: 48872

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.0240

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0263

Gnomad4 OTH AF: 0.0399

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

Aug 09, 2019

- -

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: rs113861190; hg19: chr19-13134927;