rs9922891

Variant names:

• chr16-11946654-G-A
• rs9922891
• NM_001395854.1:c.-306-8986C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-11946654-G-A
• chr16-11946654-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395854.1(NPIPB2):​c.-306-8986C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 152,120 control chromosomes in the GnomAD database, including 372 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 0.064 (372 hom., cov: 30)
• Consequence: NPIPB2 NM_001395854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 4 publications found

Genes affected

NPIPB2 (HGNC:37451): (nuclear pore complex interacting protein family member B2) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPIPB2	NM_001395854.1	c.-306-8986C>T		intron_variant	Intron 3 of 9		NP_001382783.1
NPIPB2	NM_001395855.1	c.-306-8986C>T		intron_variant	Intron 2 of 8		NP_001382784.1
NPIPB2	NM_001355514.1	c.-306-8986C>T		intron_variant	Intron 3 of 8		NP_001342443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPIPB2	ENST00000673243.1	c.-306-8986C>T		intron_variant	Intron 3 of 9			ENSP00000500799.1
NPIPB2	ENST00000538896.5	c.-583-4540C>T		intron_variant	Intron 1 of 5	5		ENSP00000442069.1
NPIPB2	ENST00000532936.1	n.307-8986C>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9710 AN: 152002 Hom.: 372 Cov.: 30

Gnomad AFR AF: 0.0416

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0513

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.0800

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

GnomAD4 genome AF: 0.0639 AC: 9716 AN: 152120 Hom.: 372 Cov.: 30 AF XY: 0.0633 AC XY: 4707 AN XY: 74350

African (AFR) AF: 0.0416 AC: 1728 AN: 41534

American (AMR) AF: 0.0880 AC: 1340 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4824

European-Finnish (FIN) AF: 0.0513 AC: 543 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0764 AC: 5191 AN: 67984

Other (OTH) AF: 0.0791 AC: 167 AN: 2110

Alfa AF: 0.0748 Hom.: 886

Bravo AF: 0.0656

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.1
DANN	Benign	0.34
PhyloP100		-0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9922891; hg19: chr16-12040511;