19-12996142-C-CGT

Position:

• chr19-12996142-C-CGT

Variant summary

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

The NM_001365902.3(NFIX):​c.27+306_27+307dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.025 (77 hom., cov: 0)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 19-12996142-C-CGT is Benign according to our data. Variant chr19-12996142-C-CGT is described in ClinVar as [Benign]. Clinvar id is 1272646.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIX	NM_001365902.3	c.27+306_27+307dup		intron_variant		ENST00000592199.6
NFIX	NM_001365982.2	c.27+306_27+307dup		intron_variant
NFIX	NM_002501.4	c.27+306_27+307dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIX	ENST00000592199.6	c.27+306_27+307dup		intron_variant		5	NM_001365902.3	P4
NFIX	ENST00000397661.6	c.27+306_27+307dup		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0249 AC: 3634 AN: 145682 Hom.: 77 Cov.: 0

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0365

Gnomad EAS AF: 0.00275

Gnomad SAS AF: 0.00545

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.0201

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0181

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

GnomAD4 genome AF: 0.0250 AC: 3644 AN: 145748 Hom.: 77 Cov.: 0 AF XY: 0.0245 AC XY: 1735 AN XY: 70816

Gnomad4 AFR AF: 0.0599

Gnomad4 AMR AF: 0.0168

Gnomad4 ASJ AF: 0.0365

Gnomad4 EAS AF: 0.00276

Gnomad4 SAS AF: 0.00481

Gnomad4 FIN AF: 0.0126

Gnomad4 NFE AF: 0.0104

Gnomad4 OTH AF: 0.0199

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

Dec 07, 2020

- -

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;