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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-138303627-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=138303627&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NME9",
"hgnc_id": 21343,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Ser",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_001349018.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": 0.3765,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.03,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8555442094802856,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 330,
"aa_ref": "G",
"aa_start": 270,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2150,
"cdna_start": 1324,
"cds_end": null,
"cds_length": 993,
"cds_start": 808,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001349018.2",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000333911.9",
"protein_coding": true,
"protein_id": "NP_001335947.1",
"strand": false,
"transcript": "NM_001349018.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 330,
"aa_ref": "G",
"aa_start": 270,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2150,
"cdna_start": 1324,
"cds_end": null,
"cds_length": 993,
"cds_start": 808,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000333911.9",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001349018.2",
"protein_coding": true,
"protein_id": "ENSP00000335444.3",
"strand": false,
"transcript": "ENST00000333911.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1118,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000492993.5",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "n.470G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000419355.1",
"strand": false,
"transcript": "ENST00000492993.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 330,
"aa_ref": "G",
"aa_start": 270,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1608,
"cdna_start": 1006,
"cds_end": null,
"cds_length": 993,
"cds_start": 808,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000953094.1",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623153.1",
"strand": false,
"transcript": "ENST00000953094.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 291,
"aa_ref": "G",
"aa_start": 231,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1618,
"cdna_start": 792,
"cds_end": null,
"cds_length": 876,
"cds_start": 691,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001349024.2",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.691G>A",
"hgvs_p": "p.Gly231Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335953.1",
"strand": false,
"transcript": "NM_001349024.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 291,
"aa_ref": "G",
"aa_start": 231,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2033,
"cdna_start": 1207,
"cds_end": null,
"cds_length": 876,
"cds_start": 691,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001349025.2",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.691G>A",
"hgvs_p": "p.Gly231Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335954.1",
"strand": false,
"transcript": "NM_001349025.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 291,
"aa_ref": "G",
"aa_start": 231,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1717,
"cdna_start": 891,
"cds_end": null,
"cds_length": 876,
"cds_start": 691,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000953093.1",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.691G>A",
"hgvs_p": "p.Gly231Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623152.1",
"strand": false,
"transcript": "ENST00000953093.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 269,
"aa_ref": "G",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2131,
"cdna_start": 1305,
"cds_end": null,
"cds_length": 810,
"cds_start": 625,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001349022.2",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335951.1",
"strand": false,
"transcript": "NM_001349022.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 267,
"aa_ref": "G",
"aa_start": 207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1961,
"cdna_start": 1135,
"cds_end": null,
"cds_length": 804,
"cds_start": 619,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001349020.2",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.619G>A",
"hgvs_p": "p.Gly207Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335949.1",
"strand": false,
"transcript": "NM_001349020.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 263,
"aa_ref": "G",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2099,
"cdna_start": 828,
"cds_end": null,
"cds_length": 792,
"cds_start": 625,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_178130.4",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_835231.1",
"strand": false,
"transcript": "NM_178130.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 263,
"aa_ref": "G",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1930,
"cdna_start": 660,
"cds_end": null,
"cds_length": 792,
"cds_start": 625,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000317876.8",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000321929.4",
"strand": false,
"transcript": "ENST00000317876.8",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 263,
"aa_ref": "G",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2133,
"cdna_start": 863,
"cds_end": null,
"cds_length": 792,
"cds_start": 625,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000383180.6",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000372667.2",
"strand": false,
"transcript": "ENST00000383180.6",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 261,
"aa_ref": "G",
"aa_start": 207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2406,
"cdna_start": 1135,
"cds_end": null,
"cds_length": 786,
"cds_start": 619,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001349021.2",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.619G>A",
"hgvs_p": "p.Gly207Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335950.1",
"strand": false,
"transcript": "NM_001349021.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 261,
"aa_ref": "G",
"aa_start": 207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 825,
"cdna_start": 658,
"cds_end": null,
"cds_length": 786,
"cds_start": 619,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000484930.5",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.619G>A",
"hgvs_p": "p.Gly207Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419882.1",
"strand": false,
"transcript": "ENST00000484930.5",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 240,
"aa_ref": "G",
"aa_start": 180,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1975,
"cdna_start": 1149,
"cds_end": null,
"cds_length": 723,
"cds_start": 538,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001349023.2",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.538G>A",
"hgvs_p": "p.Gly180Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335952.1",
"strand": false,
"transcript": "NM_001349023.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 165,
"aa_ref": "R",
"aa_start": 148,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 800,
"cdna_start": 444,
"cds_end": null,
"cds_length": 498,
"cds_start": 443,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000474690.5",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.443G>A",
"hgvs_p": "p.Arg148Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420435.1",
"strand": false,
"transcript": "ENST00000474690.5",
"transcript_support_level": 3
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 318,
"aa_ref": "G",
"aa_start": 270,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2806,
"cdna_start": 1324,
"cds_end": null,
"cds_length": 957,
"cds_start": 808,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047448078.1",
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304034.1",
"strand": false,
"transcript": "XM_047448078.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs775395996",
"effect": "missense_variant",
"frequency_reference_population": 0.000004807184,
"gene_hgnc_id": 21343,
"gene_symbol": "NME9",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000480718,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.228,
"pos": 138303627,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.477,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001349018.2"
}
]
}