rs1065663

Variant names:

• chr16-1789022-G-A
• rs1065663
• NM_012225.4:c.*308G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-1789022-G-A
• chr16-1789022-G-C

Variant summary

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

The NM_012225.4(NUBP2):​c.*308G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 347,590 control chromosomes in the GnomAD database, including 114,771 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 0.84 (53928 hom., cov: 35)
  • Exomes 𝑓: 0.79 (60843 hom.)
• Consequence: NUBP2 NM_012225.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

NUBP2 (HGNC:8042): (NUBP iron-sulfur cluster assembly factor 2, cytosolic) This gene encodes an adenosine triphosphate (ATP) and metal-binding protein that is required for the assembly of cyotosolic iron-sulfur proteins. The encoded protein functions in a heterotetramer with nucleotide-binding protein 1 (NUBP1). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2013]

SPSB3 (HGNC:30629): (splA/ryanodine receptor domain and SOCS box containing 3) Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be located in cytosol. Predicted to be part of SCF ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUBP2	NM_012225.4	c.*308G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000262302.14	NP_036357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUBP2	ENST00000262302.14	c.*308G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_012225.4	ENSP00000262302.9

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127518 AN: 152180 Hom.: 53869 Cov.: 35

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.850

GnomAD4 exome AF: 0.786 AC: 153528 AN: 195292 Hom.: 60843 Cov.: 2 AF XY: 0.782 AC XY: 78848 AN XY: 100820

Gnomad4 AFR exome AF: 0.935

Gnomad4 AMR exome AF: 0.785

Gnomad4 ASJ exome AF: 0.839

Gnomad4 EAS exome AF: 0.650

Gnomad4 SAS exome AF: 0.719

Gnomad4 FIN exome AF: 0.718

Gnomad4 NFE exome AF: 0.804

Gnomad4 OTH exome AF: 0.802

GnomAD4 genome AF: 0.838 AC: 127636 AN: 152298 Hom.: 53928 Cov.: 35 AF XY: 0.829 AC XY: 61740 AN XY: 74470

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.850

Alfa AF: 0.825 Hom.: 68401

Bravo AF: 0.854

Asia WGS AF: 0.737 AC: 2564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.096
DANN	Benign	0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1065663; hg19: chr16-1839023;