9-127546749-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NIBAN2	NM_022833.4	c.56-14971A>G		intron_variant		ENST00000373312.4
NIBAN2	NM_001035534.3	c.17-14971A>G		intron_variant
NIBAN2	XM_005252135.3	c.274+14399A>G		intron_variant
NIBAN2	XM_011518925.2	c.145+14399A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIBAN2	ENST00000373312.4	c.56-14971A>G		intron_variant		1	NM_022833.4	P1

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

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.442

Alfa AF: 0.417 Hom.: 6819

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891730; hg19: chr9-130309028;