rs201731717

Variant names:

• chr19-13023630-CTTTTTTTTTTT-C
• rs201731717
• NM_001365902.3:c.28-1386_28-1376delTTTTTTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr19-13023630-CTTTTTTTTTTT-C
• chr19-13023630-CTTTTTTTTTTT-CT
• chr19-13023630-CTTTTTTTTTTT-CTT
• chr19-13023630-CTTTTTTTTTTT-CTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTTTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTTTTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTTTTTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTTTTTTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTTTTTTTTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTTTTTTTTTTT
• chr19-13023630-CTTTTTTTTTTT-CTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001365902.3(NFIX):​c.28-1386_28-1376delTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000777 in 128,670 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000078 (0 hom., cov: 26)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 0 publications found

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]

NFIX Gene-Disease associations (from GenCC):

• Malan overgrowth syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina, ClinGen, Orphanet
• Marshall-Smith syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Illumina, G2P, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365902.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFIX	NM_001365902.3	MANE Select	c.28-1386_28-1376delTTTTTTTTTTT		intron	N/A	NP_001352831.1	Q14938-1
	NFIX	NM_002501.4		c.28-1386_28-1376delTTTTTTTTTTT		intron	N/A	NP_002492.2	Q14938-3
	NFIX	NM_001365982.2		c.28-1386_28-1376delTTTTTTTTTTT		intron	N/A	NP_001352911.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFIX	ENST00000592199.6	TSL:5 MANE Select	c.28-1390_28-1380delTTTTTTTTTTT		intron	N/A	ENSP00000467512.1	Q14938-1
	NFIX	ENST00000397661.6	TSL:5	c.28-1390_28-1380delTTTTTTTTTTT		intron	N/A	ENSP00000380781.2	Q14938-3
	NFIX	ENST00000590027.1	TSL:2	c.-114-1390_-114-1380delTTTTTTTTTTT		intron	N/A	ENSP00000465616.1	K7EKH0

Frequencies

GnomAD3 genomes AF: 0.00000777 AC: 1 AN: 128670 Hom.: 0 Cov.: 26

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: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000166

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00000777 AC: 1 AN: 128670 Hom.: 0 Cov.: 26 AF XY: 0.0000161 AC XY: 1 AN XY: 61980

African (AFR) AF: 0.00 AC: 0 AN: 34060

American (AMR) AF: 0.00 AC: 0 AN: 12856

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3092

East Asian (EAS) AF: 0.00 AC: 0 AN: 4332

South Asian (SAS) AF: 0.00 AC: 0 AN: 4006

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7186

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.0000166 AC: 1 AN: 60362

Other (OTH) AF: 0.00 AC: 0 AN: 1720

Alfa AF: 0.00 Hom.: 46

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs201731717; hg19: chr19-13134444;