Variant chr1-149072872-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_001388367.1(NBPF9):c.1152G>A(p.Leu384Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,449,618 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00034 ( 1 hom., cov: 29)

Exomes 𝑓: 0.00018 ( 25 hom. )

Failed GnomAD Quality Control

Consequence

NBPF9
NM_001388367.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.450

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-149072872-C-T is Benign according to our data. Variant chr1-149072872-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3067318.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.45 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 25 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBPF9	NM_001388367.1 linkuse as main transcript	c.1152G>A	p.Leu384Leu	synonymous_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.1152G>A	p.Leu384Leu	synonymous_variant	14/30		NM_001388367.1	ENSP00000513968.1		P0DPF3-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

147930

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000170

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000403

Gnomad ASJ

AF:

0.000909

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.000425

Gnomad FIN

AF:

0.000295

Gnomad MID

AF:

0.00338

Gnomad NFE

AF:

0.000396

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00259

AC:

641

AN:

247150

Hom.:

AF XY:

0.00256

AC XY:

344

AN XY:

134128

show subpopulations

Gnomad AFR exome

AF:

0.00141

Gnomad AMR exome

AF:

0.00272

Gnomad ASJ exome

AF:

0.00365

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.00191

Gnomad FIN exome

AF:

0.000702

Gnomad NFE exome

AF:

0.00340

Gnomad OTH exome

AF:

0.00517

GnomAD4 exome

AF:

0.000184

AC:

267

AN:

1449618

Hom.:

Cov.:

AF XY:

0.000209

AC XY:

151

AN XY:

721314

show subpopulations

Gnomad4 AFR exome

AF:

0.000390

Gnomad4 AMR exome

AF:

0.0000224

Gnomad4 ASJ exome

AF:

0.000310

Gnomad4 EAS exome

AF:

0.000454

Gnomad4 SAS exome

AF:

0.000384

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000152

Gnomad4 OTH exome

AF:

0.000368

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000344

AC:

AN:

148048

Hom.:

Cov.:

AF XY:

0.000360

AC XY:

AN XY:

72316

show subpopulations

Gnomad4 AFR

AF:

0.000218

Gnomad4 AMR

AF:

0.000403

Gnomad4 ASJ

AF:

0.000909

Gnomad4 EAS

AF:

0.000195

Gnomad4 SAS

AF:

0.000425

Gnomad4 FIN

AF:

0.000295

Gnomad4 NFE

AF:

0.000396

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00850

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: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.31

DANN

Benign

0.58

Splicing

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