rs2382470

chr9-14387818-A-G

Variant summary

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

The NM_001369458.1(NFIB):c.97-80298T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,092 control chromosomes in the GnomAD database, including 45,731 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 0.77 (45731 hom., cov: 31)
• Consequence: NFIB NM_001369458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

NFIB (HGNC:7785): (nuclear factor I B) Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and transcription regulator inhibitor activity. Involved in brain development; negative regulation of DNA binding activity; and regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIB	NM_001190738.2	c.108+10706T>C		intron_variant
NFIB	NM_001369458.1	c.97-80298T>C		intron_variant
NFIB	NM_001369459.1	c.97-80298T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIB	ENST00000380934.8	c.108+10706T>C		intron_variant		2
NFIB	ENST00000638165.1	n.188+10706T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117693 AN: 151974 Hom.: 45688 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.774 AC: 117788 AN: 152092 Hom.: 45731 Cov.: 31 AF XY: 0.774 AC XY: 57544 AN XY: 74340

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.761

Alfa AF: 0.760 Hom.: 88590

Bravo AF: 0.773

Asia WGS AF: 0.759 AC: 2640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.96
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2382470; hg19: chr9-14387817;