rs497501

Variant names:

• chr16-28646303-C-T
• rs497501
• NM_001310136.2:c.121-1832C>T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPIPB8	NM_001310136.2	c.121-1832C>T		intron_variant	Intron 2 of 7	ENST00000683297.1	NP_001297065.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPIPB8	ENST00000683297.1	c.121-1832C>T		intron_variant	Intron 2 of 7		NM_001310136.2	ENSP00000507410.1
NPIPB8	ENST00000529716.5	c.121-1832C>T		intron_variant	Intron 1 of 6	5		ENSP00000434399.1

Frequencies

GnomAD3 genomes AF: 0.0143 AC: 1653 AN: 115274 Hom.: 0 Cov.: 15

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0853 AC: 1575 AN: 18456

American (AMR) AF: 0.00408 AC: 50 AN: 12250

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3284

East Asian (EAS) AF: 0.00211 AC: 9 AN: 4256

South Asian (SAS) AF: 0.000813 AC: 3 AN: 3688

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8586

Middle Eastern (MID) AF: 0.00382 AC: 1 AN: 262

European-Non Finnish (NFE) AF: 0.0000644 AC: 4 AN: 62160

Other (OTH) AF: 0.0117 AC: 19 AN: 1626

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		0.14

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

Other links and lift over

dbSNP: rs497501; hg19: chr16-28657624;