19-13024113-CAAAAAAA-CAAAAAAAAAA

Variant names:

• chr19-13024113-C-CAAA
• rs113861190
• NM_001365902.3:c.28-893_28-891dupAAA

Variant summary

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

The NM_001365902.3(NFIX):​c.28-893_28-891dupAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00185 in 411,290 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 0.000019 (0 hom., cov: 28)
  • Exomes 𝑓: 0.0025 (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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 758 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3	c.28-893_28-891dupAAA		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_28-907insAAA		intron_variant	Intron 1 of 10	5	NM_001365902.3	ENSP00000467512.1

Frequencies

GnomAD3 genomes AF: 0.0000292 AC: 3 AN: 102670 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.000103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00246 AC: 758 AN: 308614 Hom.: 0 AF XY: 0.00241 AC XY: 401 AN XY: 166316

Gnomad4 AFR exome AF: 0.00469

Gnomad4 AMR exome AF: 0.00409

Gnomad4 ASJ exome AF: 0.00238

Gnomad4 EAS exome AF: 0.00259

Gnomad4 SAS exome AF: 0.00315

Gnomad4 FIN exome AF: 0.00202

Gnomad4 NFE exome AF: 0.00220

Gnomad4 OTH exome AF: 0.00246

GnomAD4 genome AF: 0.0000195 AC: 2 AN: 102676 Hom.: 0 Cov.: 28 AF XY: 0.0000204 AC XY: 1 AN XY: 48914

Gnomad4 AFR AF: 0.0000683

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;