rs2257055

chr9-127549125-A-Cchr9-127549125-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIBAN2	NM_022833.4	c.56-17347T>G		intron_variant		ENST00000373312.4
NIBAN2	NM_001035534.3	c.17-17347T>G		intron_variant
NIBAN2	XM_005252135.3	c.274+12023T>G		intron_variant
NIBAN2	XM_011518925.2	c.145+12023T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIBAN2	ENST00000373312.4	c.56-17347T>G		intron_variant		1	NM_022833.4	P1

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

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.427

Alfa AF: 0.480 Hom.: 24616

Bravo AF: 0.411

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.3
Dann	Benign	0.81

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: rs2257055; hg19: chr9-130311404; COSMIC: COSV64824067;