chr16-11953042-C-T

Variant names:

• chr16-11953042-C-T
• rs7185307
• NM_001395854.1:c.-307+3102G>A

Variant summary

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

The NM_001395854.1(NPIPB2):​c.-307+3102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,074 control chromosomes in the GnomAD database, including 29,541 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 0.58 (29541 hom., cov: 32)
• Consequence: NPIPB2 NM_001395854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPIPB2	NM_001395854.1	c.-307+3102G>A		intron_variant	Intron 3 of 9		NP_001382783.1
NPIPB2	NM_001395855.1	c.-307+3102G>A		intron_variant	Intron 2 of 8		NP_001382784.1
NPIPB2	NM_001355514.1	c.-307+3102G>A		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.-307+3102G>A		intron_variant	Intron 3 of 9			ENSP00000500799.1
NPIPB2	ENST00000538896.5	c.-583-10928G>A		intron_variant	Intron 1 of 5	5		ENSP00000442069.1
NPIPB2	ENST00000532936.1	n.306+3102G>A		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88199 AN: 151956 Hom.: 29540 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.580 AC: 88205 AN: 152074 Hom.: 29541 Cov.: 32 AF XY: 0.577 AC XY: 42879 AN XY: 74348

African (AFR) AF: 0.239 AC: 9893 AN: 41460

American (AMR) AF: 0.492 AC: 7503 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2429 AN: 3468

East Asian (EAS) AF: 0.598 AC: 3094 AN: 5176

South Asian (SAS) AF: 0.666 AC: 3207 AN: 4818

European-Finnish (FIN) AF: 0.716 AC: 7567 AN: 10568

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52301 AN: 68004

Other (OTH) AF: 0.611 AC: 1290 AN: 2112

Alfa AF: 0.691 Hom.: 119785

Bravo AF: 0.544

Asia WGS AF: 0.539 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.5
DANN	Benign	0.83
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7185307; hg19: chr16-12046899;