chr1-146126300-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001302371.3(NBPF10):c.1962G>A(p.Gln654Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000208 in 1,585,122 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 0.000033 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
NBPF10
NM_001302371.3 synonymous
NM_001302371.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.825
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BP6
Variant 1-146126300-C-T is Benign according to our data. Variant chr1-146126300-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2639091.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.825 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NBPF10 | ENST00000583866.9 | c.1962G>A | p.Gln654Gln | synonymous_variant | Exon 14 of 90 | 5 | NM_001302371.3 | ENSP00000463957.6 | ||
NBPF10 | ENST00000617010.2 | c.-5914G>A | 5_prime_UTR_variant | Exon 14 of 91 | 5 | ENSP00000479344.2 | ||||
NBPF10 | ENST00000612520.2 | c.1853+728G>A | intron_variant | Intron 18 of 20 | 5 | ENSP00000483006.2 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151706Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000127 AC: 3AN: 236266Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128876
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GnomAD4 exome AF: 0.0000195 AC: 28AN: 1433300Hom.: 0 Cov.: 28 AF XY: 0.0000210 AC XY: 15AN XY: 714738
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 151822Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74222
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
NBPF10: BP4, BP7 -
Computational scores
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Name
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at