rs931067

Variant names:

• chr19-13047969-G-A
• rs931067
• NM_001365902.3:c.559+22417G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-13047969-G-A
• chr19-13047969-G-C

Variant summary

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

The NM_001365902.3(NFIX):​c.559+22417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,074 control chromosomes in the GnomAD database, including 7,157 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 0.29 (7157 hom., cov: 32)
• Consequence: NFIX NM_001365902.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIX	NM_001365902.3	c.559+22417G>A		intron_variant	Intron 2 of 10	ENST00000592199.6	NP_001352831.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIX	ENST00000592199.6	c.559+22417G>A		intron_variant	Intron 2 of 10	5	NM_001365902.3	ENSP00000467512.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43763 AN: 151956 Hom.: 7163 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.288 AC: 43767 AN: 152074 Hom.: 7157 Cov.: 32 AF XY: 0.295 AC XY: 21933 AN XY: 74362

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.305

Alfa AF: 0.297 Hom.: 9695

Bravo AF: 0.295

Asia WGS AF: 0.468 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.68

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: rs931067; hg19: chr19-13158783;