NM_001365902.3:c.27+302_27+307delTGTGTG

Variant names:

• chr19-12996142-CGTGTGT-C
• rs3046151
• NM_001365902.3:c.27+302_27+307delTGTGTG

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001365902.3(NFIX):​c.27+302_27+307delTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0012 (1 hom., cov: 0)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 169 AD gene.

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.27+302_27+307delTGTGTG		intron	N/A	NP_001352831.1	Q14938-1
	NFIX	NM_002501.4		c.27+302_27+307delTGTGTG		intron	N/A	NP_002492.2	Q14938-3
	NFIX	NM_001365982.2		c.27+302_27+307delTGTGTG		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.27+279_27+284delGTGTGT		intron	N/A	ENSP00000467512.1	Q14938-1
	NFIX	ENST00000397661.6	TSL:5	c.27+279_27+284delGTGTGT		intron	N/A	ENSP00000380781.2	Q14938-3

Frequencies

GnomAD3 genomes AF: 0.00116 AC: 169 AN: 145710 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000653

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00183

Gnomad ASJ AF: 0.000294

Gnomad EAS AF: 0.00317

Gnomad SAS AF: 0.000436

Gnomad FIN AF: 0.000629

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00134

Gnomad OTH AF: 0.00202

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

GnomAD4 genome AF: 0.00116 AC: 169 AN: 145776 Hom.: 1 Cov.: 0 AF XY: 0.00104 AC XY: 74 AN XY: 70830

African (AFR) AF: 0.000651 AC: 26 AN: 39938

American (AMR) AF: 0.00183 AC: 27 AN: 14786

Ashkenazi Jewish (ASJ) AF: 0.000294 AC: 1 AN: 3396

East Asian (EAS) AF: 0.00318 AC: 15 AN: 4718

South Asian (SAS) AF: 0.000438 AC: 2 AN: 4570

European-Finnish (FIN) AF: 0.000629 AC: 6 AN: 9544

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00134 AC: 88 AN: 65660

Other (OTH) AF: 0.00199 AC: 4 AN: 2006

Alfa AF: 0.000222 Hom.: 686

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs3046151; hg19: chr19-13106956;