19-13024113-CAAAAAAA-CAAAAA

Variant names:

• chr19-13024113-CAA-C
• rs113861190
• NM_001365902.3:c.28-892_28-891delAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001365902.3(NFIX):​c.28-892_28-891delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 404,852 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0011 (0 hom., cov: 28)
  • Exomes 𝑓: 0.020 (0 hom.)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96

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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.0204 (6155/302200) while in subpopulation AFR AF= 0.0246 (175/7116). AF 95% confidence interval is 0.0217. There are 0 homozygotes in gnomad4_exome. There are 3359 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 108 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3	c.28-892_28-891delAA		intron_variant	Intron 1 of 10	ENST00000592199.6	NP_001352831.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIX	ENST00000592199.6	c.28-907_28-906delAA		intron_variant	Intron 1 of 10	5	NM_001365902.3	ENSP00000467512.1

Frequencies

GnomAD3 genomes AF: 0.00104 AC: 107 AN: 102646 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00294

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000511

Gnomad ASJ AF: 0.000393

Gnomad EAS AF: 0.000281

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000201

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000275

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0204 AC: 6155 AN: 302200 Hom.: 0 AF XY: 0.0206 AC XY: 3359 AN XY: 162914

Gnomad4 AFR exome AF: 0.0246

Gnomad4 AMR exome AF: 0.0242

Gnomad4 ASJ exome AF: 0.0240

Gnomad4 EAS exome AF: 0.0205

Gnomad4 SAS exome AF: 0.0194

Gnomad4 FIN exome AF: 0.0209

Gnomad4 NFE exome AF: 0.0199

Gnomad4 OTH exome AF: 0.0216

GnomAD4 genome AF: 0.00105 AC: 108 AN: 102652 Hom.: 0 Cov.: 28 AF XY: 0.00119 AC XY: 58 AN XY: 48896

Gnomad4 AFR AF: 0.00297

Gnomad4 AMR AF: 0.000511

Gnomad4 ASJ AF: 0.000393

Gnomad4 EAS AF: 0.000283

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000201

Gnomad4 NFE AF: 0.000275

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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;