rs2039052

Variant names:

• chr9-14435337-C-A
• rs2039052
• NM_001369458.1:c.96+96610G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-14435337-C-A
• chr9-14435337-C-G
• chr9-14435337-C-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+96610G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,078 control chromosomes in the GnomAD database, including 8,827 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 0.32 (8827 hom., cov: 33)
• Consequence: NFIB NM_001369458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIB	NM_001369458.1	c.96+96610G>T		intron_variant	Intron 1 of 11		NP_001356387.1
NFIB	NM_001369459.1	c.96+96610G>T		intron_variant	Intron 1 of 11		NP_001356388.1
NFIB	NM_001369462.1	c.96+96610G>T		intron_variant	Intron 1 of 9		NP_001356391.1
NFIB	NM_001369468.1	c.96+96610G>T		intron_variant	Intron 1 of 8		NP_001356397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIB-AS1	ENST00000659981.1	n.416+28849C>A		intron_variant	Intron 3 of 3
NFIB-AS1	ENST00000842090.1	n.226-10734C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49105 AN: 151960 Hom.: 8816 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.323 AC: 49147 AN: 152078 Hom.: 8827 Cov.: 33 AF XY: 0.329 AC XY: 24425 AN XY: 74318

African (AFR) AF: 0.173 AC: 7186 AN: 41488

American (AMR) AF: 0.470 AC: 7175 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2038 AN: 5168

South Asian (SAS) AF: 0.285 AC: 1377 AN: 4824

European-Finnish (FIN) AF: 0.449 AC: 4739 AN: 10556

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24507 AN: 67972

Other (OTH) AF: 0.344 AC: 727 AN: 2114

Alfa AF: 0.263 Hom.: 1004

Bravo AF: 0.321

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.27
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs2039052; hg19: chr9-14435335;