rs1008943

Variant names:

• chr9-14434740-T-A
• rs1008943
• NM_001369458.1:c.96+97207A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001369458.1(NFIB):​c.96+97207A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,138 control chromosomes in the GnomAD database, including 9,464 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 0.34 (9464 hom., cov: 33)
• Consequence: NFIB NM_001369458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 2 publications found

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]

NFIB-AS1 (HGNC:56058): (NFIB antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001369458.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFIB	NM_001369458.1		c.96+97207A>T		intron	N/A	NP_001356387.1
	NFIB	NM_001369459.1		c.96+97207A>T		intron	N/A	NP_001356388.1
	NFIB	NM_001369462.1		c.96+97207A>T		intron	N/A	NP_001356391.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFIB-AS1	ENST00000659981.1		n.416+28252T>A		intron	N/A
	NFIB-AS1	ENST00000842090.1		n.226-11331T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51921 AN: 152020 Hom.: 9452 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.342 AC: 51968 AN: 152138 Hom.: 9464 Cov.: 33 AF XY: 0.346 AC XY: 25746 AN XY: 74374

African (AFR) AF: 0.228 AC: 9450 AN: 41500

American (AMR) AF: 0.483 AC: 7381 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2056 AN: 5178

South Asian (SAS) AF: 0.287 AC: 1387 AN: 4828

European-Finnish (FIN) AF: 0.449 AC: 4742 AN: 10562

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24783 AN: 67998

Other (OTH) AF: 0.354 AC: 746 AN: 2108

Alfa AF: 0.342 Hom.: 1134

Bravo AF: 0.341

Asia WGS AF: 0.355 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.44
DANN	Benign	0.65
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1008943; hg19: chr9-14434738;