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GeneBe

1-149072872-C-T

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.Leu384=) 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

2

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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.45 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 25 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NBPF9NM_001388367.1 linkuse as main transcriptc.1152G>A p.Leu384= synonymous_variant 14/30 ENST00000698832.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NBPF9ENST00000698832.1 linkuse as main transcriptc.1152G>A p.Leu384= synonymous_variant 14/30 NM_001388367.1 P1P0DPF3-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00
AC:
49
AN:
147930
Hom.:
1
Cov.:
29
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.:
25
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.:
25
Cov.:
32
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
?
    Genome Aggregation Database, over 76,156 genomes
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000344
AC:
51
AN:
148048
Hom.:
1
Cov.:
29
AF XY:
0.000360
AC XY:
26
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.:
5

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2024NBPF9: 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.

Other links and lift over

dbSNP: rs199626513; hg19: chr1-148337472; COSMIC: COSV56014826; API