rs10489584

Positions:

• chr1-184919880-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIBAN1	NM_052966.4	c.56-20571C>T		intron_variant		ENST00000367511.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIBAN1	ENST00000367511.4	c.56-20571C>T		intron_variant		1	NM_052966.4	P1

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

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.00521

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00371

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.00456

Gnomad4 NFE AF: 0.00743

Gnomad4 OTH AF: 0.00860

Alfa AF: 0.00906 Hom.: 6

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

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: rs10489584; hg19: chr1-184889013;