9-127546749-T-C

Variant names:

• chr9-127546749-T-C
• rs1891730
• NM_022833.4:c.56-14971A>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.56-14971A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,738 control chromosomes in the GnomAD database, including 18,974 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 0.48 (18974 hom., cov: 30)
• Consequence: NIBAN2 NM_022833.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIBAN2	NM_022833.4	c.56-14971A>G		intron_variant	Intron 1 of 13	ENST00000373312.4	NP_073744.2
NIBAN2	NM_001035534.3	c.17-14971A>G		intron_variant	Intron 1 of 13		NP_001030611.1
NIBAN2	XM_005252135.3	c.274+14399A>G		intron_variant	Intron 2 of 14		XP_005252192.3
NIBAN2	XM_011518925.2	c.145+14399A>G		intron_variant	Intron 2 of 14		XP_011517227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIBAN2	ENST00000373312.4	c.56-14971A>G		intron_variant	Intron 1 of 13	1	NM_022833.4	ENSP00000362409.3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73123 AN: 151618 Hom.: 18934 Cov.: 30

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.483 AC: 73222 AN: 151738 Hom.: 18974 Cov.: 30 AF XY: 0.488 AC XY: 36212 AN XY: 74130

African (AFR) AF: 0.628 AC: 25987 AN: 41352

American (AMR) AF: 0.539 AC: 8234 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3472

East Asian (EAS) AF: 0.803 AC: 4084 AN: 5088

South Asian (SAS) AF: 0.594 AC: 2855 AN: 4804

European-Finnish (FIN) AF: 0.364 AC: 3834 AN: 10528

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25406 AN: 67924

Other (OTH) AF: 0.442 AC: 929 AN: 2104

Alfa AF: 0.416 Hom.: 7581

Bravo AF: 0.504

Asia WGS AF: 0.635 AC: 2211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.56
PhyloP100		1.1
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: rs1891730; hg19: chr9-130309028;