rs11085829

chr19-13063498-G-Achr19-13063498-G-Cchr19-13063498-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365902.3(NFIX):c.560-9549G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 150,372 control chromosomes in the GnomAD database, including 19,844 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (19844 hom., cov: 29)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIX	NM_001365902.3	c.560-9549G>A		intron_variant		ENST00000592199.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIX	ENST00000592199.6	c.560-9549G>A		intron_variant		5	NM_001365902.3	P4

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72170 AN: 150264 Hom.: 19805 Cov.: 29

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.480 AC: 72253 AN: 150372 Hom.: 19844 Cov.: 29 AF XY: 0.481 AC XY: 35253 AN XY: 73262

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.458

Alfa AF: 0.376 Hom.: 14862

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.25
Dann	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11085829; hg19: chr19-13174312;