rs10489584

Variant names:

• chr1-184919880-G-A
• rs10489584
• NM_052966.4:c.56-20571C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_052966.4(NIBAN1):​c.56-20571C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 151,166 control chromosomes in the GnomAD database, including 17 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 0.011 (17 hom., cov: 31)
• Consequence: NIBAN1 NM_052966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 0 publications found

Genes affected

NIBAN1 (HGNC:16784): (niban apoptosis regulator 1) This gene encodes a member of the family with sequence similarity 129 protein family. This gene is highly expressed in several cancer cells and may serve as a prognostic marker for certain cancers. The encoded protein may play a role in regulating p53-mediated apoptosis. [provided by RefSeq, Sep 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0108 (1639/151166) while in subpopulation AFR AF = 0.0201 (828/41188). AF 95% confidence interval is 0.019. There are 17 homozygotes in GnomAd4. There are 811 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIBAN1	NM_052966.4	c.56-20571C>T		intron_variant	Intron 1 of 13	ENST00000367511.4	NP_443198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIBAN1	ENST00000367511.4	c.56-20571C>T		intron_variant	Intron 1 of 13	1	NM_052966.4	ENSP00000356481.3

Frequencies

GnomAD3 genomes AF: 0.0109 AC: 1642 AN: 151048 Hom.: 17 Cov.: 31

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.00528

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00371

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.00456

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00743

Gnomad OTH AF: 0.00869

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

GnomAD4 genome AF: 0.0108 AC: 1639 AN: 151166 Hom.: 17 Cov.: 31 AF XY: 0.0110 AC XY: 811 AN XY: 73768

African (AFR) AF: 0.0201 AC: 828 AN: 41188

American (AMR) AF: 0.00521 AC: 79 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.000289 AC: 1 AN: 3464

East Asian (EAS) AF: 0.00371 AC: 19 AN: 5116

South Asian (SAS) AF: 0.0199 AC: 95 AN: 4762

European-Finnish (FIN) AF: 0.00456 AC: 47 AN: 10310

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00743 AC: 504 AN: 67856

Other (OTH) AF: 0.00860 AC: 18 AN: 2094

Alfa AF: 0.00897 Hom.: 8

Bravo AF: 0.0108

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.62
DANN	Benign	0.62
PhyloP100		-0.049
Mutation Taster		=100/0	polymorphism

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: rs10489584; hg19: chr1-184889013;