Variant 1-149079092-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001388367.1(NBPF9):c.408G>A(p.Pro136=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000989 in 133,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00099 ( 0 hom., cov: 24)

Exomes 𝑓: 0.0037 ( 7 hom. )

Failed GnomAD Quality Control

Consequence

NBPF9
NM_001388367.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.32

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

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

BP6

Variant 1-149079092-C-T is Benign according to our data. Variant chr1-149079092-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2639058.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.32 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NBPF9	NM_001388367.1 linkuse as main transcript	c.408G>A	p.Pro136=	synonymous_variant	9/30	ENST00000698832.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NBPF9	ENST00000698832.1 linkuse as main transcript	c.408G>A	p.Pro136=	synonymous_variant	9/30		NM_001388367.1	P1	P0DPF3-1

Frequencies

GnomAD3 genomes

AF:

0.000990

AC:

132

AN:

133354

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00132

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000522

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00293

Gnomad SAS

AF:

0.00801

Gnomad FIN

AF:

0.000534

Gnomad MID

AF:

0.00327

Gnomad NFE

AF:

0.000422

Gnomad OTH

AF:

0.00231

GnomAD3 exomes

AF:

0.000117

AC:

AN:

247314

Hom.:

AF XY:

0.000111

AC XY:

AN XY:

134634

show subpopulations

Gnomad AFR exome

AF:

0.000273

Gnomad AMR exome

AF:

0.000203

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000197

Gnomad FIN exome

AF:

0.0000463

Gnomad NFE exome

AF:

0.0000896

Gnomad OTH exome

AF:

0.000166

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00368

AC:

4113

AN:

1116156

Hom.:

Cov.:

AF XY:

0.00514

AC XY:

2907

AN XY:

565212

show subpopulations

Gnomad4 AFR exome

AF:

0.00272

Gnomad4 AMR exome

AF:

0.00108

Gnomad4 ASJ exome

AF:

0.000971

Gnomad4 EAS exome

AF:

0.00714

Gnomad4 SAS exome

AF:

0.00741

Gnomad4 FIN exome

AF:

0.0115

Gnomad4 NFE exome

AF:

0.00292

Gnomad4 OTH exome

AF:

0.00486

GnomAD4 genome

AF:

0.000989

AC:

132

AN:

133466

Hom.:

Cov.:

AF XY:

0.00118

AC XY:

AN XY:

64490

show subpopulations

Gnomad4 AFR

AF:

0.00131

Gnomad4 AMR

AF:

0.000521

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00294

Gnomad4 SAS

AF:

0.00802

Gnomad4 FIN

AF:

0.000534

Gnomad4 NFE

AF:

0.000422

Gnomad4 OTH

AF:

0.00229

Alfa

AF:

0.000843

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, 2022

NBPF9: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

7.2

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