9-127549125-A-C

Variant names:

• chr9-127549125-A-C
• rs2257055
• NM_022833.4:c.56-17347T>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.56-17347T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,066 control chromosomes in the GnomAD database, including 13,930 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 0.41 (13930 hom., cov: 32)
• Consequence: NIBAN2 NM_022833.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022833.4. 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
	NIBAN2	NM_022833.4	MANE Select	c.56-17347T>G		intron	N/A	NP_073744.2
	NIBAN2	NM_001035534.3		c.17-17347T>G		intron	N/A	NP_001030611.1	Q96TA1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIBAN2	ENST00000373312.4	TSL:1 MANE Select	c.56-17347T>G		intron	N/A	ENSP00000362409.3	Q96TA1-1
	NIBAN2	ENST00000373314.7	TSL:1	c.17-17347T>G		intron	N/A	ENSP00000362411.3	Q96TA1-2
	NIBAN2	ENST00000484348.2	TSL:1	n.162+19790T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61949 AN: 151948 Hom.: 13933 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.407 AC: 61963 AN: 152066 Hom.: 13930 Cov.: 32 AF XY: 0.401 AC XY: 29856 AN XY: 74366

African (AFR) AF: 0.220 AC: 9137 AN: 41506

American (AMR) AF: 0.462 AC: 7059 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1598 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1987 AN: 5154

South Asian (SAS) AF: 0.401 AC: 1932 AN: 4818

European-Finnish (FIN) AF: 0.366 AC: 3875 AN: 10596

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34677 AN: 67928

Other (OTH) AF: 0.427 AC: 901 AN: 2112

Alfa AF: 0.471 Hom.: 32980

Bravo AF: 0.411

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.81
PhyloP100		0.39
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: rs2257055; hg19: chr9-130311404; COSMIC: COSV64824067;