rs497501

Positions:

• chr16-28646303-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001310136.2(NPIPB8):​c.121-1832C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.014 (0 hom., cov: 15)
  • Failed GnomAD Quality Control
• Consequence: NPIPB8 NM_001310136.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

Genes affected

NPIPB8 (HGNC:37490): (nuclear pore complex interacting protein family member B8) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPIPB8	NM_001310136.2	c.121-1832C>T		intron_variant		ENST00000683297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPIPB8	ENST00000683297.1	c.121-1832C>T		intron_variant			NM_001310136.2	P1
NPIPB8	ENST00000529716.5	c.121-1832C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1653 AN: 115274 Hom.: 0 Cov.: 15 FAILED QC

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00417

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.000814

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00355

Gnomad NFE AF: 0.0000643

Gnomad OTH AF: 0.0112

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0144 AC: 1661 AN: 115336 Hom.: 0 Cov.: 15 AF XY: 0.0140 AC XY: 782 AN XY: 55710

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.00408

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00211

Gnomad4 SAS AF: 0.000813

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000644

Gnomad4 OTH AF: 0.0117

Alfa AF: 0.0441 Hom.: 15

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.90

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: rs497501; hg19: chr16-28657624;