rs520605

Positions:

• chr1-184826645-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052966.4(NIBAN1):​c.718-2903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,130 control chromosomes in the GnomAD database, including 47,240 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 0.78 (47240 hom., cov: 32)
• Consequence: NIBAN1 NM_052966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

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]

LOC107985238 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIBAN1	NM_052966.4	c.718-2903G>A		intron_variant		ENST00000367511.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIBAN1	ENST00000367511.4	c.718-2903G>A		intron_variant		1	NM_052966.4	P1
NIBAN1	ENST00000461167.1	n.812-2903G>A		intron_variant, non_coding_transcript_variant		3
NIBAN1	ENST00000487074.5	n.295-3316G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118893 AN: 152012 Hom.: 47178 Cov.: 32

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.782 AC: 119011 AN: 152130 Hom.: 47240 Cov.: 32 AF XY: 0.776 AC XY: 57704 AN XY: 74356

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.768

Alfa AF: 0.755 Hom.: 82777

Bravo AF: 0.792

Asia WGS AF: 0.651 AC: 2264 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	5.3
DANN	Benign	0.65

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: rs520605; hg19: chr1-184795779;