19-13024113-CAAAAAAA-CAAAAAAAAA

Variant names:

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

Variant summary

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

The NM_001365902.3(NFIX):​c.28-892_28-891dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 405,930 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 0.0022 (0 hom., cov: 28)
  • Exomes 𝑓: 0.024 (0 hom.)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.0242 (7348/303270) while in subpopulation AFR AF= 0.0353 (250/7090). AF 95% confidence interval is 0.0317. There are 0 homozygotes in gnomad4_exome. There are 3972 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 226 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3	c.28-892_28-891dupAA		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.28-908_28-907insAA		intron_variant	Intron 1 of 10	5	NM_001365902.3	ENSP00000467512.1

Frequencies

GnomAD3 genomes AF: 0.00219 AC: 225 AN: 102654 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00629

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000613

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00225

Gnomad SAS AF: 0.000322

Gnomad FIN AF: 0.000603

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000444

Gnomad OTH AF: 0.00149

GnomAD4 exome AF: 0.0242 AC: 7348 AN: 303270 Hom.: 0 AF XY: 0.0243 AC XY: 3972 AN XY: 163402

Gnomad4 AFR exome AF: 0.0353

Gnomad4 AMR exome AF: 0.0306

Gnomad4 ASJ exome AF: 0.0208

Gnomad4 EAS exome AF: 0.0233

Gnomad4 SAS exome AF: 0.0331

Gnomad4 FIN exome AF: 0.0244

Gnomad4 NFE exome AF: 0.0221

Gnomad4 OTH exome AF: 0.0248

GnomAD4 genome AF: 0.00220 AC: 226 AN: 102660 Hom.: 0 Cov.: 28 AF XY: 0.00233 AC XY: 114 AN XY: 48902

Gnomad4 AFR AF: 0.00632

Gnomad4 AMR AF: 0.000613

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00226

Gnomad4 SAS AF: 0.000323

Gnomad4 FIN AF: 0.000603

Gnomad4 NFE AF: 0.000444

Gnomad4 OTH AF: 0.00148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;