rs2249110

Variant names:

• chr9-127567376-T-C
• rs2249110
• NM_022833.4:c.55+1444A>G

Variant summary

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

The NM_022833.4(NIBAN2):​c.55+1444A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,086 control chromosomes in the GnomAD database, including 26,273 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 0.58 (26273 hom., cov: 32)
• Consequence: NIBAN2 NM_022833.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 3 publications found

Genes affected

NIBAN2 (HGNC:25282): (niban apoptosis regulator 2) Enables transcription coactivator activity. Involved in several processes, including gonadotropin secretion; positive regulation of transcription regulatory region DNA binding activity; and regulation of cellular macromolecule biosynthetic process. Located in several cellular components, including adherens junction; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIBAN2	NM_022833.4	c.55+1444A>G		intron_variant	Intron 1 of 13	ENST00000373312.4	NP_073744.2
NIBAN2	NM_001035534.3	c.16+11546A>G		intron_variant	Intron 1 of 13		NP_001030611.1
NIBAN2	XM_011518925.2	c.55+1444A>G		intron_variant	Intron 1 of 14		XP_011517227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIBAN2	ENST00000373312.4	c.55+1444A>G		intron_variant	Intron 1 of 13	1	NM_022833.4	ENSP00000362409.3

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87524 AN: 151968 Hom.: 26239 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.576 AC: 87618 AN: 152086 Hom.: 26273 Cov.: 32 AF XY: 0.570 AC XY: 42372 AN XY: 74304

African (AFR) AF: 0.740 AC: 30736 AN: 41516

American (AMR) AF: 0.558 AC: 8523 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1688 AN: 3466

East Asian (EAS) AF: 0.469 AC: 2417 AN: 5154

South Asian (SAS) AF: 0.608 AC: 2931 AN: 4820

European-Finnish (FIN) AF: 0.426 AC: 4509 AN: 10592

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34984 AN: 67946

Other (OTH) AF: 0.545 AC: 1150 AN: 2112

Alfa AF: 0.547 Hom.: 3062

Bravo AF: 0.591

Asia WGS AF: 0.579 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.59
PhyloP100		-0.051
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2249110; hg19: chr9-130329655;