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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: X-16590804-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=16590804&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 16590804,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_019857.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "NM_175859.3",
"protein_id": "NP_787055.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000359276.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_175859.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000359276.9",
"protein_id": "ENSP00000352222.4",
"transcript_support_level": 1,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_175859.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359276.9"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000380241.7",
"protein_id": "ENSP00000369590.3",
"transcript_support_level": 1,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000380241.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "n.242G>A",
"hgvs_p": null,
"transcript": "ENST00000483053.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000483053.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1837G>A",
"hgvs_p": "p.Glu613Lys",
"transcript": "ENST00000944988.1",
"protein_id": "ENSP00000615047.1",
"transcript_support_level": null,
"aa_start": 613,
"aa_end": null,
"aa_length": 615,
"cds_start": 1837,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944988.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "NM_001144002.2",
"protein_id": "NP_001137474.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001144002.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "NM_019857.5",
"protein_id": "NP_062831.3",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019857.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000443824.5",
"protein_id": "ENSP00000401264.1",
"transcript_support_level": 2,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000443824.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870414.1",
"protein_id": "ENSP00000540473.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870414.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870415.1",
"protein_id": "ENSP00000540474.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870415.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870416.1",
"protein_id": "ENSP00000540475.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870416.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870417.1",
"protein_id": "ENSP00000540476.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870417.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870418.1",
"protein_id": "ENSP00000540477.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870418.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870419.1",
"protein_id": "ENSP00000540478.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870419.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870421.1",
"protein_id": "ENSP00000540480.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870421.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870422.1",
"protein_id": "ENSP00000540481.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870422.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870424.1",
"protein_id": "ENSP00000540483.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870424.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870425.1",
"protein_id": "ENSP00000540484.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870425.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000870428.1",
"protein_id": "ENSP00000540487.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870428.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000913873.1",
"protein_id": "ENSP00000583932.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913873.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000913875.1",
"protein_id": "ENSP00000583934.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913875.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys",
"transcript": "ENST00000944979.1",
"protein_id": "ENSP00000615038.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
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"aa_start": 584,
"aa_end": null,
"aa_length": 586,
"cds_start": 1750,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442261.1"
}
],
"gene_symbol": "CTPS2",
"gene_hgnc_id": 2520,
"dbsnp": "rs770159997",
"frequency_reference_population": 0.0000073797605,
"hom_count_reference_population": 4,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000737976,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06279471516609192,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.09,
"revel_prediction": "Benign",
"alphamissense_score": 0.1163,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.334,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_019857.5",
"gene_symbol": "CTPS2",
"hgnc_id": 2520,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Glu584Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}