15-73116673-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002499.4(NEO1):c.264A>G(p.Lys88=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000376 in 1,614,014 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 1 hom. )
Consequence
NEO1
NM_002499.4 synonymous
NM_002499.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.84
Genes affected
NEO1 (HGNC:7754): (neogenin 1) This gene encodes a cell surface protein that is a member of the immunoglobulin superfamily. The encoded protein consists of four N-terminal immunoglobulin-like domains, six fibronectin type III domains, a transmembrane domain and a C-terminal internal domain that shares homology with the tumor suppressor candidate gene DCC. This protein may be involved in cell growth and differentiation and in cell-cell adhesion. Defects in this gene are associated with cell proliferation in certain cancers. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 15-73116673-A-G is Benign according to our data. Variant chr15-73116673-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3045473.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.84 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEO1 | NM_002499.4 | c.264A>G | p.Lys88= | synonymous_variant | 2/29 | ENST00000261908.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEO1 | ENST00000261908.11 | c.264A>G | p.Lys88= | synonymous_variant | 2/29 | 1 | NM_002499.4 | A2 | |
NEO1 | ENST00000558964.5 | c.264A>G | p.Lys88= | synonymous_variant | 2/28 | 1 | P4 | ||
NEO1 | ENST00000560262.5 | c.264A>G | p.Lys88= | synonymous_variant | 2/28 | 1 | |||
NEO1 | ENST00000339362.9 | c.264A>G | p.Lys88= | synonymous_variant | 3/30 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00212 AC: 323AN: 152152Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000446 AC: 112AN: 250956Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135642
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GnomAD4 exome AF: 0.000195 AC: 285AN: 1461744Hom.: 1 Cov.: 31 AF XY: 0.000157 AC XY: 114AN XY: 727156
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GnomAD4 genome ? AF: 0.00211 AC: 322AN: 152270Hom.: 2 Cov.: 32 AF XY: 0.00227 AC XY: 169AN XY: 74452
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NEO1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 07, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at