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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-53082879-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53082879&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53082879,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_022117.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "NM_022117.4",
"protein_id": "NP_071400.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 693,
"cds_start": 381,
"cds_end": null,
"cds_length": 2082,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000375442.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022117.4"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000375442.8",
"protein_id": "ENSP00000364591.4",
"transcript_support_level": 1,
"aa_start": 127,
"aa_end": null,
"aa_length": 693,
"cds_start": 381,
"cds_end": null,
"cds_length": 2082,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022117.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375442.8"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000912653.1",
"protein_id": "ENSP00000582712.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 718,
"cds_start": 381,
"cds_end": null,
"cds_length": 2157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912653.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000887608.1",
"protein_id": "ENSP00000557667.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 704,
"cds_start": 381,
"cds_end": null,
"cds_length": 2115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887608.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000966749.1",
"protein_id": "ENSP00000636808.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 699,
"cds_start": 381,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966749.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000887609.1",
"protein_id": "ENSP00000557668.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 697,
"cds_start": 381,
"cds_end": null,
"cds_length": 2094,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887609.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000966747.1",
"protein_id": "ENSP00000636806.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 694,
"cds_start": 381,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966747.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000887610.1",
"protein_id": "ENSP00000557669.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 691,
"cds_start": 381,
"cds_end": null,
"cds_length": 2076,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887610.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000966750.1",
"protein_id": "ENSP00000636809.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 690,
"cds_start": 381,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966750.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000912652.1",
"protein_id": "ENSP00000582711.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 675,
"cds_start": 381,
"cds_end": null,
"cds_length": 2028,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912652.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000966748.1",
"protein_id": "ENSP00000636807.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 653,
"cds_start": 381,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966748.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "ENST00000966751.1",
"protein_id": "ENSP00000636810.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 607,
"cds_start": 381,
"cds_end": null,
"cds_length": 1824,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966751.1"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "XM_017029726.2",
"protein_id": "XP_016885215.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 738,
"cds_start": 381,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029726.2"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "XM_017029727.2",
"protein_id": "XP_016885216.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 737,
"cds_start": 381,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029727.2"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "XM_006724592.5",
"protein_id": "XP_006724655.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 694,
"cds_start": 381,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724592.5"
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg",
"transcript": "XM_047442353.1",
"protein_id": "XP_047298309.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 380,
"cds_start": 381,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442353.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.168+213C>G",
"hgvs_p": null,
"transcript": "ENST00000887607.1",
"protein_id": "ENSP00000557666.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 491,
"cds_start": null,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887607.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.168+213C>G",
"hgvs_p": null,
"transcript": "ENST00000887611.1",
"protein_id": "ENSP00000557670.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 454,
"cds_start": null,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000887611.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "c.168+213C>G",
"hgvs_p": null,
"transcript": "ENST00000579390.1",
"protein_id": "ENSP00000462287.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": null,
"cds_end": null,
"cds_length": 751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000579390.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "n.513C>G",
"hgvs_p": null,
"transcript": "ENST00000553557.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000553557.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "n.-115C>G",
"hgvs_p": null,
"transcript": "ENST00000578306.5",
"protein_id": "ENSP00000462635.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000578306.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"hgvs_c": "n.-244C>G",
"hgvs_p": null,
"transcript": "ENST00000556808.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000556808.1"
}
],
"gene_symbol": "TSPYL2",
"gene_hgnc_id": 24358,
"dbsnp": "rs782528598",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 9.11303e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20047777891159058,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.042,
"revel_prediction": "Benign",
"alphamissense_score": 0.4512,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.64,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.046,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_022117.4",
"gene_symbol": "TSPYL2",
"hgnc_id": 24358,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.381C>G",
"hgvs_p": "p.Ser127Arg"
}
],
"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
}