Variant chr1-16581452-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_001405667.2(NBPF1):c.1347G>A(p.Glu449Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 0 hom., cov: 80)

Exomes 𝑓: 0.00020 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NBPF1
NM_001405667.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.58

Variant links:

Genes affected

NBPF1 (HGNC:26088): (NBPF member 1) 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]

NBPF1 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=-0.85).

BP6

Variant 1-16581452-C-T is Benign according to our data. Variant chr1-16581452-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638363.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.58 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
NBPF1	NM_001405667.2 linkuse as main transcript	c.1347G>A	p.Glu449Glu	synonymous_variant	15/29	NP_001392596.1
NBPF1	NM_001405680.2 linkuse as main transcript	c.1347G>A	p.Glu449Glu	synonymous_variant	15/29	NP_001392609.1
NBPF1	NM_001405681.2 linkuse as main transcript	c.1347G>A	p.Glu449Glu	synonymous_variant	15/29	NP_001392610.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
NBPF1	ENST00000430580.6 linkuse as main transcript	c.1347G>A	p.Glu449Glu	synonymous_variant	15/29	5	ENSP00000474456.1	Q3BBV0-2
NBPF1	ENST00000392963.5 linkuse as main transcript	n.*215G>A		non_coding_transcript_exon_variant	6/19	5	ENSP00000473795.1	S4R2Z6
NBPF1	ENST00000392963.5 linkuse as main transcript	n.*215G>A		3_prime_UTR_variant	6/19	5	ENSP00000473795.1	S4R2Z6

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

434

AN:

127202

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00821

Gnomad AMI

AF:

0.00123

Gnomad AMR

AF:

0.00372

Gnomad ASJ

AF:

0.00100

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00253

Gnomad FIN

AF:

0.00186

Gnomad MID

AF:

0.00385

Gnomad NFE

AF:

0.00151

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.0000609

AC:

AN:

246278

Hom.:

AF XY:

0.0000749

AC XY:

AN XY:

133552

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000297

Gnomad ASJ exome

AF:

0.000204

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000236

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000447

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000196

AC:

270

AN:

1377242

Hom.:

Cov.:

124

AF XY:

0.000196

AC XY:

134

AN XY:

684938

show subpopulations

Gnomad4 AFR exome

AF:

0.000507

Gnomad4 AMR exome

AF:

0.00101

Gnomad4 ASJ exome

AF:

0.000207

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000352

Gnomad4 FIN exome

AF:

0.000156

Gnomad4 NFE exome

AF:

0.000154

Gnomad4 OTH exome

AF:

0.000158

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00341

AC:

434

AN:

127254

Hom.:

Cov.:

AF XY:

0.00351

AC XY:

219

AN XY:

62396

show subpopulations

Gnomad4 AFR

AF:

0.00819

Gnomad4 AMR

AF:

0.00372

Gnomad4 ASJ

AF:

0.00100

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00253

Gnomad4 FIN

AF:

0.00186

Gnomad4 NFE

AF:

0.00151

Gnomad4 OTH

AF:

0.00333

Alfa

AF:

0.0118

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

Sep 01, 2023

NBPF1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.8

DANN

Benign

0.69

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