Variant chr16-15370093-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001277325.2(NPIPA5):c.219G>A(p.Pro73=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00214 in 1,547,522 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 6 hom., cov: 20)

Exomes 𝑓: 0.0022 ( 81 hom. )

Consequence

NPIPA5
NM_001277325.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.704

Variant links:

Genes affected

NPIPA5 (HGNC:41980): (nuclear pore complex interacting protein family member A5) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPIPA5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 16-15370093-C-T is Benign according to our data. Variant chr16-15370093-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646249.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.704 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPIPA5	NM_001277325.2 linkuse as main transcript	c.219G>A	p.Pro73=	synonymous_variant	3/8	ENST00000360151.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPIPA5	ENST00000360151.9 linkuse as main transcript	c.219G>A	p.Pro73=	synonymous_variant	3/8	1	NM_001277325.2		E9PKD4-1
NPIPA5	ENST00000543801.5 linkuse as main transcript	c.219G>A	p.Pro73=	synonymous_variant	3/8	1			E9PKD4-2
NPIPA5	ENST00000534094.1 linkuse as main transcript	c.276G>A	p.Pro92=	synonymous_variant	3/7	5		P1

Frequencies

GnomAD3 genomes

AF:

0.00195

AC:

269

AN:

137656

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000891

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00124

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00127

Gnomad FIN

AF:

0.000469

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00324

Gnomad OTH

AF:

0.00109

GnomAD3 exomes

AF:

0.00120

AC:

AN:

64426

Hom.:

AF XY:

0.00131

AC XY:

AN XY:

32126

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00104

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000257

Gnomad SAS exome

AF:

0.000859

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00200

Gnomad OTH exome

AF:

0.000931

GnomAD4 exome

AF:

0.00216

AC:

3044

AN:

1409762

Hom.:

Cov.:

AF XY:

0.00211

AC XY:

1483

AN XY:

702836

show subpopulations

Gnomad4 AFR exome

AF:

0.000515

Gnomad4 AMR exome

AF:

0.000833

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000159

Gnomad4 SAS exome

AF:

0.00133

Gnomad4 FIN exome

AF:

0.000653

Gnomad4 NFE exome

AF:

0.00253

Gnomad4 OTH exome

AF:

0.00158

GnomAD4 genome

AF:

0.00195

AC:

269

AN:

137760

Hom.:

Cov.:

AF XY:

0.00166

AC XY:

110

AN XY:

66150

show subpopulations

Gnomad4 AFR

AF:

0.000888

Gnomad4 AMR

AF:

0.00124

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00127

Gnomad4 FIN

AF:

0.000469

Gnomad4 NFE

AF:

0.00324

Gnomad4 OTH

AF:

0.00107

Alfa

AF:

0.000554

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

Feb 01, 2023

NPIPA5: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.7

DANN

Benign

0.59

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