19-13023630-CTTTTTTTT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001365902.3(NFIX):c.28-1383_28-1376del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 128,650 control chromosomes in the GnomAD database, including 723 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (723 hom., cov: 26)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.435

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 Benign. Variant got -10 ACMG points.

• BP6: Variant 19-13023630-CTTTTTTTT-C is Benign according to our data. Variant chr19-13023630-CTTTTTTTT-C is described in ClinVar as [Benign]. Clinvar id is 1283288.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIX	NM_001365902.3	c.28-1383_28-1376del		intron_variant		ENST00000592199.6
NFIX	NM_001365982.2	c.28-1383_28-1376del		intron_variant
NFIX	NM_002501.4	c.28-1383_28-1376del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIX	ENST00000592199.6	c.28-1383_28-1376del		intron_variant		5	NM_001365902.3	P4
NFIX	ENST00000397661.6	c.28-1383_28-1376del		intron_variant		5
NFIX	ENST00000590027.1	c.-114-1383_-114-1376del		intron_variant		2
NFIX	ENST00000585382.5	c.-114-1383_-114-1376del		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0999 AC: 12856 AN: 128638 Hom.: 720 Cov.: 26

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.0114

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.0621

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0526

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0901

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

GnomAD4 genome AF: 0.100 AC: 12864 AN: 128650 Hom.: 723 Cov.: 26 AF XY: 0.0979 AC XY: 6068 AN XY: 61984

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.0621

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.0823

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.0924

Bravo AF: 0.0802

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 02, 2019

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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: rs201731717; hg19: chr19-13134444;