Variant 16-29383273-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001310137.5(NPIPB11):c.1659G>C(p.Ala553Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.012 ( 14 hom., cov: 20)

Exomes 𝑓: 0.0040 ( 286 hom. )

Failed GnomAD Quality Control

Consequence

NPIPB11
NM_001310137.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.32

Variant links:

Genes affected

NPIPB11 (HGNC:37453): (nuclear pore complex interacting protein family member B11) Predicted to act upstream of or within prevention of polyspermy. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPIPB11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 16-29383273-C-G is Benign according to our data. Variant chr16-29383273-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2672626.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.32 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0122 (1454/119156) while in subpopulation NFE AF= 0.0183 (985/53778). AF 95% confidence interval is 0.0174. There are 14 homozygotes in gnomad4. There are 672 alleles in male gnomad4 subpopulation. Median coverage is 20. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
NPIPB11	NM_001310137.5 linkuse as main transcript	c.1659G>C	p.Ala553Ala	synonymous_variant	8/8	ENST00000698511.1	NP_001297066.2
NPIPB11	XM_047434576.1 linkuse as main transcript	c.1659G>C	p.Ala553Ala	synonymous_variant	7/8		XP_047290532.1
NPIPB11	XM_047434577.1 linkuse as main transcript	c.1293G>C	p.Ala431Ala	synonymous_variant	8/9		XP_047290533.1
NPIPB11	XM_047434578.1 linkuse as main transcript	c.1236G>C	p.Ala412Ala	synonymous_variant	8/9		XP_047290534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPIPB11	ENST00000698511.1 linkuse as main transcript	c.1659G>C	p.Ala553Ala	synonymous_variant	8/8		NM_001310137.5	ENSP00000513761.1		E5RHQ5
NPIPB11	ENST00000524087.5 linkuse as main transcript	c.1659G>C	p.Ala553Ala	synonymous_variant	8/8	5		ENSP00000430853.1		E5RHQ5

Frequencies

GnomAD3 genomes

AF:

0.0122

AC:

1454

AN:

119062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00355

Gnomad AMI

AF:

0.00581

Gnomad AMR

AF:

0.0109

Gnomad ASJ

AF:

0.0277

Gnomad EAS

AF:

0.000932

Gnomad SAS

AF:

0.00392

Gnomad FIN

AF:

0.0146

Gnomad MID

AF:

0.00505

Gnomad NFE

AF:

0.0183

Gnomad OTH

AF:

0.0106

GnomAD3 exomes

AF:

0.00407

AC:

907

AN:

222842

Hom.:

AF XY:

0.00393

AC XY:

478

AN XY:

121638

show subpopulations

Gnomad AFR exome

AF:

0.00195

Gnomad AMR exome

AF:

0.00383

Gnomad ASJ exome

AF:

0.00435

Gnomad EAS exome

AF:

0.000225

Gnomad SAS exome

AF:

0.00172

Gnomad FIN exome

AF:

0.00714

Gnomad NFE exome

AF:

0.00531

Gnomad OTH exome

AF:

0.00384

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00395

AC:

5474

AN:

1385182

Hom.:

286

Cov.:

AF XY:

0.00411

AC XY:

2826

AN XY:

688004

show subpopulations

Gnomad4 AFR exome

AF:

0.00168

Gnomad4 AMR exome

AF:

0.00325

Gnomad4 ASJ exome

AF:

0.0112

Gnomad4 EAS exome

AF:

0.0000255

Gnomad4 SAS exome

AF:

0.00176

Gnomad4 FIN exome

AF:

0.0163

Gnomad4 NFE exome

AF:

0.00357

Gnomad4 OTH exome

AF:

0.00578

GnomAD4 genome

AF:

0.0122

AC:

1454

AN:

119156

Hom.:

Cov.:

AF XY:

0.0116

AC XY:

672

AN XY:

57882

show subpopulations

Gnomad4 AFR

AF:

0.00354

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.0277

Gnomad4 EAS

AF:

0.000934

Gnomad4 SAS

AF:

0.00393

Gnomad4 FIN

AF:

0.0146

Gnomad4 NFE

AF:

0.0183

Gnomad4 OTH

AF:

0.0106

Alfa

AF:

0.0139

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

NPIPB11: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.9

DANN

Benign

0.49

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over