chr1-146066405-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001302371.3(NBPF10):c.11301C>T(p.Phe3767=) 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 0.013 ( 5 hom., cov: 11)
Exomes 𝑓: 0.0065 ( 27 hom. )
Failed GnomAD Quality Control
Consequence
NBPF10
NM_001302371.3 synonymous
NM_001302371.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.46
Genes affected
NBPF10 (HGNC:31992): (NBPF member 10) 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.07).
BP6
Variant 1-146066405-G-A is Benign according to our data. Variant chr1-146066405-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2639107.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.46 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.00652 (4849/743280) while in subpopulation AFR AF= 0.0307 (615/20004). AF 95% confidence interval is 0.0287. There are 27 homozygotes in gnomad4_exome. There are 2560 alleles in male gnomad4_exome subpopulation. Median coverage is 10. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 27 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NBPF10 | NM_001302371.3 | c.11301C>T | p.Phe3767= | synonymous_variant | 90/90 | ENST00000583866.9 | |
NBPF10 | NM_001039703.6 | c.10794C>T | p.Phe3598= | synonymous_variant | 86/86 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBPF10 | ENST00000583866.9 | c.11301C>T | p.Phe3767= | synonymous_variant | 90/90 | 5 | NM_001302371.3 | P1 | |
NBPF10 | ENST00000617010.2 | c.3633C>T | p.Phe1211= | synonymous_variant | 91/91 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1264AN: 99898Hom.: 5 Cov.: 11 FAILED QC
GnomAD3 genomes
AF:
AC:
1264
AN:
99898
Hom.:
Cov.:
11
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00694 AC: 1731AN: 249484Hom.: 0 AF XY: 0.00675 AC XY: 912AN XY: 135072
GnomAD3 exomes
AF:
AC:
1731
AN:
249484
Hom.:
AF XY:
AC XY:
912
AN XY:
135072
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00652 AC: 4849AN: 743280Hom.: 27 Cov.: 10 AF XY: 0.00675 AC XY: 2560AN XY: 379204
GnomAD4 exome
AF:
AC:
4849
AN:
743280
Hom.:
Cov.:
10
AF XY:
AC XY:
2560
AN XY:
379204
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0126 AC: 1263AN: 99998Hom.: 5 Cov.: 11 AF XY: 0.0126 AC XY: 582AN XY: 46082
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1263
AN:
99998
Hom.:
Cov.:
11
AF XY:
AC XY:
582
AN XY:
46082
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
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 | Dec 01, 2022 | NBPF10: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at