19-12996142-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGT

Variant names:

• chr19-12996142-CGTGTGTGT-C
• rs3046151
• NM_001365902.3:c.27+300_27+307delTGTGTGTG

Variant summary

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

The NM_001365902.3(NFIX):​c.27+300_27+307delTGTGTGTG 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 0.0017 (1 hom., cov: 0)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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 245 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3	c.27+300_27+307delTGTGTGTG		intron_variant	Intron 1 of 10	ENST00000592199.6	NP_001352831.1
NFIX	NM_002501.4	c.27+300_27+307delTGTGTGTG		intron_variant	Intron 1 of 9		NP_002492.2
NFIX	NM_001365982.2	c.27+300_27+307delTGTGTGTG		intron_variant	Intron 1 of 8		NP_001352911.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIX	ENST00000592199.6	c.27+279_27+286delGTGTGTGT		intron_variant	Intron 1 of 10	5	NM_001365902.3	ENSP00000467512.1
NFIX	ENST00000397661.6	c.27+279_27+286delGTGTGTGT		intron_variant	Intron 1 of 9	5		ENSP00000380781.2

Frequencies

GnomAD3 genomes AF: 0.00168 AC: 245 AN: 145720 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000703

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00250

Gnomad ASJ AF: 0.000294

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000436

Gnomad FIN AF: 0.000105

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00262

Gnomad OTH AF: 0.00202

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

GnomAD4 genome AF: 0.00168 AC: 245 AN: 145786 Hom.: 1 Cov.: 0 AF XY: 0.00157 AC XY: 111 AN XY: 70832

Gnomad4 AFR AF: 0.000701

Gnomad4 AMR AF: 0.00250

Gnomad4 ASJ AF: 0.000294

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000438

Gnomad4 FIN AF: 0.000105

Gnomad4 NFE AF: 0.00262

Gnomad4 OTH AF: 0.00199

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: rs3046151; hg19: chr19-13106956;