rs682331

Positions:

• chr1-184792231-A-G
• chr1-184792231-A-T

Variant summary

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

The NM_052966.4(NIBAN1):​c.*2746T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,050 control chromosomes in the GnomAD database, including 22,278 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 0.53 (22277 hom., cov: 32)
  • Exomes 𝑓: 0.44 (1 hom.)
• Consequence: NIBAN1 NM_052966.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIBAN1	NM_052966.4	c.*2746T>C		3_prime_UTR_variant	14/14	ENST00000367511.4	NP_443198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIBAN1	ENST00000367511	c.*2746T>C		3_prime_UTR_variant	14/14	1	NM_052966.4	ENSP00000356481.3
NIBAN1	ENST00000417056.5	c.260-1166T>C		intron_variant		3		ENSP00000414039.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80291 AN: 151914 Hom.: 22252 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.505

GnomAD4 exome AF: 0.444 AC: 8 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.417 AC XY: 5 AN XY: 12

Gnomad4 AFR exome AF: 0.750

Gnomad4 NFE exome AF: 0.357

GnomAD4 genome AF: 0.529 AC: 80361 AN: 152032 Hom.: 22277 Cov.: 32 AF XY: 0.531 AC XY: 39503 AN XY: 74324

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.500

Alfa AF: 0.442 Hom.: 13914

Bravo AF: 0.533

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.62
DANN	Benign	0.60

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: rs682331; hg19: chr1-184761365; COSMIC: COSV62283715; COSMIC: COSV62283715;