chr1-146125486-T-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001302371.3(NBPF10):c.2057A>T(p.Asp686Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 5/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00063 ( 2 hom., cov: 9)
Exomes 𝑓: 0.00067 ( 3 hom. )
Consequence
NBPF10
NM_001302371.3 missense
NM_001302371.3 missense
Scores
1
4
Clinical Significance
Conservation
PhyloP100: -1.44
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.030658394).
BP6
Variant 1-146125486-T-A is Benign according to our data. Variant chr1-146125486-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2639093.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NBPF10 | NM_001302371.3 | c.2057A>T | p.Asp686Val | missense_variant | 15/90 | ENST00000583866.9 | |
NBPF10 | NM_001039703.6 | c.2057A>T | p.Asp686Val | missense_variant | 15/86 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBPF10 | ENST00000583866.9 | c.2057A>T | p.Asp686Val | missense_variant | 15/90 | 5 | NM_001302371.3 | P1 | |
NBPF10 | ENST00000617010.2 | c.-5819A>T | 5_prime_UTR_variant | 15/91 | 5 | ||||
NBPF10 | ENST00000612520.2 | c.1853+1542A>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000626 AC: 45AN: 71870Hom.: 2 Cov.: 9
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GnomAD3 exomes AF: 0.000575 AC: 30AN: 52142Hom.: 1 AF XY: 0.000498 AC XY: 13AN XY: 26098
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GnomAD4 exome AF: 0.000669 AC: 260AN: 388812Hom.: 3 Cov.: 0 AF XY: 0.000648 AC XY: 138AN XY: 212966
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GnomAD4 genome AF: 0.000626 AC: 45AN: 71902Hom.: 2 Cov.: 9 AF XY: 0.000597 AC XY: 20AN XY: 33482
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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
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | NBPF10: BP4, BS2 - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
LIST_S2
Benign
T
MetaRNN
Benign
T
Sift4G
Pathogenic
D
Vest4
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at