rs338565

Positions:

• chr1-184807967-G-A

Variant summary

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

The NM_052966.4(NIBAN1):​c.1335+107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,290,532 control chromosomes in the GnomAD database, including 39,958 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 0.29 (7624 hom., cov: 32)
  • Exomes 𝑓: 0.22 (32334 hom.)
• Consequence: NIBAN1 NM_052966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIBAN1	NM_052966.4	c.1335+107C>T		intron_variant		ENST00000367511.4	NP_443198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIBAN1	ENST00000367511.4	c.1335+107C>T		intron_variant		1	NM_052966.4	ENSP00000356481	P1
NIBAN1	ENST00000487074.5	n.807+107C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44650 AN: 151942 Hom.: 7616 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.271

GnomAD3 exomes AF: 0.274 AC: 66182 AN: 241832 Hom.: 10286 AF XY: 0.266 AC XY: 34903 AN XY: 131074

Gnomad AFR exome AF: 0.457

Gnomad AMR exome AF: 0.319

Gnomad ASJ exome AF: 0.138

Gnomad EAS exome AF: 0.467

Gnomad SAS exome AF: 0.306

Gnomad FIN exome AF: 0.303

Gnomad NFE exome AF: 0.200

Gnomad OTH exome AF: 0.243

GnomAD4 exome AF: 0.223 AC: 253521 AN: 1138472 Hom.: 32334 Cov.: 15 AF XY: 0.224 AC XY: 129630 AN XY: 579254

Gnomad4 AFR exome AF: 0.454

Gnomad4 AMR exome AF: 0.318

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.478

Gnomad4 SAS exome AF: 0.301

Gnomad4 FIN exome AF: 0.293

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.235

GnomAD4 genome AF: 0.294 AC: 44707 AN: 152060 Hom.: 7624 Cov.: 32 AF XY: 0.297 AC XY: 22104 AN XY: 74328

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.269

Alfa AF: 0.250 Hom.: 1414

Bravo AF: 0.302

Asia WGS AF: 0.400 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs338565; hg19: chr1-184777101; COSMIC: COSV62283634; COSMIC: COSV62283634;