Variant 1-149072882-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001388367.1(NBPF9):c.1142G>A(p.Arg381Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000060 ( 0 hom., cov: 29)

Exomes 𝑓: 0.000016 ( 4 hom. )

Failed GnomAD Quality Control

Consequence

NBPF9
NM_001388367.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0300

Variant links:

Genes affected

NBPF9 (HGNC:31991): (NBPF member 9) This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. [provided by RefSeq, Apr 2013]

NBPF9 links:

NBPF9 (HGNC:):

NBPF9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.054292142).

BP6

Variant 1-149072882-C-T is Benign according to our data. Variant chr1-149072882-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3067405.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBPF9	NM_001388367.1 linkuse as main transcript	c.1142G>A	p.Arg381Lys	missense_variant	14/30	ENST00000698832.1	NP_001375296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NBPF9	ENST00000698832.1 linkuse as main transcript	c.1142G>A	p.Arg381Lys	missense_variant	14/30		NM_001388367.1	ENSP00000513968.1		P0DPF3-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

149274

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000295

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000211

Gnomad FIN

AF:

0.0000973

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000903

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00144

AC:

356

AN:

246958

Hom.:

AF XY:

0.00149

AC XY:

200

AN XY:

134044

show subpopulations

Gnomad AFR exome

AF:

0.000834

Gnomad AMR exome

AF:

0.00187

Gnomad ASJ exome

AF:

0.00122

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000889

Gnomad FIN exome

AF:

0.000373

Gnomad NFE exome

AF:

0.00194

Gnomad OTH exome

AF:

0.00268

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000158

AC:

AN:

1454114

Hom.:

Cov.:

AF XY:

0.0000207

AC XY:

AN XY:

723514

show subpopulations

Gnomad4 AFR exome

AF:

0.0000300

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.000116

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000697

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000903

Gnomad4 OTH exome

AF:

0.0000500

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000602

AC:

AN:

149390

Hom.:

Cov.:

AF XY:

0.0000685

AC XY:

AN XY:

72960

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000295

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000211

Gnomad4 FIN

AF:

0.0000973

Gnomad4 NFE

AF:

0.0000903

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00743

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

Mar 01, 2024

NBPF9: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Benign

-0.39

CADD

Benign

0.34

DANN

Benign

0.63

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0031

LIST_S2

Benign

0.41

.;T;T;T;T;T;T;.

M_CAP

Benign

0.0065

MetaRNN

Benign

0.054

T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.64

Sift4G

Benign

0.46

T;T;T;T;T;T;T;T

Vest4

0.31

MutPred

0.30

Gain of ubiquitination at R381 (P = 0.0109);Gain of ubiquitination at R381 (P = 0.0109);Gain of ubiquitination at R381 (P = 0.0109);Gain of ubiquitination at R381 (P = 0.0109);Gain of ubiquitination at R381 (P = 0.0109);Gain of ubiquitination at R381 (P = 0.0109);.;Gain of ubiquitination at R381 (P = 0.0109);

MVP

0.32

ClinPred

0.028

GERP RS

-0.83

Varity_R

0.030

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