19-13024113-CAAAAAAA-CAAA

Variant names:

• chr19-13024113-CAAAA-C
• rs113861190
• NM_001365902.3:c.28-894_28-891delAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001365902.3(NFIX):​c.28-894_28-891delAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 411,742 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00017 (1 hom., cov: 28)
  • Exomes 𝑓: 0.0013 (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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 17 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3	c.28-894_28-891delAAAA		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_28-904delAAAA		intron_variant	Intron 1 of 10	5	NM_001365902.3	ENSP00000467512.1

Frequencies

GnomAD3 genomes AF: 0.000175 AC: 18 AN: 102670 Hom.: 1 Cov.: 28

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00354

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000127

Gnomad OTH AF: 0.000744

GnomAD4 exome AF: 0.00130 AC: 403 AN: 309066 Hom.: 0 AF XY: 0.00166 AC XY: 277 AN XY: 166604

Gnomad4 AFR exome AF: 0.000413

Gnomad4 AMR exome AF: 0.000835

Gnomad4 ASJ exome AF: 0.000793

Gnomad4 EAS exome AF: 0.000787

Gnomad4 SAS exome AF: 0.00632

Gnomad4 FIN exome AF: 0.000522

Gnomad4 NFE exome AF: 0.000658

Gnomad4 OTH exome AF: 0.000961

GnomAD4 genome AF: 0.000166 AC: 17 AN: 102676 Hom.: 1 Cov.: 28 AF XY: 0.000245 AC XY: 12 AN XY: 48912

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00323

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000127

Gnomad4 OTH AF: 0.000740

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;