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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: 9-91724414-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=91724414&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 91724414,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_004560.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.2080T>C",
"hgvs_p": "p.Cys694Arg",
"transcript": "NM_004560.4",
"protein_id": "NP_004551.2",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 943,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2832,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000375708.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004560.4"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.2080T>C",
"hgvs_p": "p.Cys694Arg",
"transcript": "ENST00000375708.4",
"protein_id": "ENSP00000364860.3",
"transcript_support_level": 1,
"aa_start": 694,
"aa_end": null,
"aa_length": 943,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2832,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004560.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375708.4"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1660T>C",
"hgvs_p": "p.Cys554Arg",
"transcript": "ENST00000375715.5",
"protein_id": "ENSP00000364867.1",
"transcript_support_level": 1,
"aa_start": 554,
"aa_end": null,
"aa_length": 704,
"cds_start": 1660,
"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": "ENST00000375715.5"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1999T>C",
"hgvs_p": "p.Cys667Arg",
"transcript": "ENST00000964760.1",
"protein_id": "ENSP00000634819.1",
"transcript_support_level": null,
"aa_start": 667,
"aa_end": null,
"aa_length": 916,
"cds_start": 1999,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964760.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1765T>C",
"hgvs_p": "p.Cys589Arg",
"transcript": "ENST00000912487.1",
"protein_id": "ENSP00000582546.1",
"transcript_support_level": null,
"aa_start": 589,
"aa_end": null,
"aa_length": 838,
"cds_start": 1765,
"cds_end": null,
"cds_length": 2517,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912487.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1519T>C",
"hgvs_p": "p.Cys507Arg",
"transcript": "ENST00000912486.1",
"protein_id": "ENSP00000582545.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 756,
"cds_start": 1519,
"cds_end": null,
"cds_length": 2271,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912486.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.2071T>C",
"hgvs_p": "p.Cys691Arg",
"transcript": "XM_017014762.2",
"protein_id": "XP_016870251.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 940,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017014762.2"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1660T>C",
"hgvs_p": "p.Cys554Arg",
"transcript": "XM_005252008.5",
"protein_id": "XP_005252065.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 803,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005252008.5"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1660T>C",
"hgvs_p": "p.Cys554Arg",
"transcript": "XM_006717121.4",
"protein_id": "XP_006717184.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 803,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717121.4"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1660T>C",
"hgvs_p": "p.Cys554Arg",
"transcript": "XM_047423434.1",
"protein_id": "XP_047279390.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 803,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423434.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1660T>C",
"hgvs_p": "p.Cys554Arg",
"transcript": "XM_047423435.1",
"protein_id": "XP_047279391.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 803,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423435.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1660T>C",
"hgvs_p": "p.Cys554Arg",
"transcript": "XM_047423436.1",
"protein_id": "XP_047279392.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 803,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423436.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1660T>C",
"hgvs_p": "p.Cys554Arg",
"transcript": "XM_047423437.1",
"protein_id": "XP_047279393.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 803,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423437.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.877T>C",
"hgvs_p": "p.Cys293Arg",
"transcript": "XM_005252009.4",
"protein_id": "XP_005252066.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 542,
"cds_start": 877,
"cds_end": null,
"cds_length": 1629,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005252009.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "n.2548T>C",
"hgvs_p": null,
"transcript": "ENST00000550066.5",
"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": "pseudogene",
"feature": "ENST00000550066.5"
}
],
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"dbsnp": "rs142386992",
"frequency_reference_population": 0.00008735659,
"hom_count_reference_population": 0,
"allele_count_reference_population": 141,
"gnomad_exomes_af": 0.0000937164,
"gnomad_genomes_af": 0.0000262784,
"gnomad_exomes_ac": 137,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8400866389274597,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.761,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8973,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.224,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004560.4",
"gene_symbol": "ROR2",
"hgnc_id": 10257,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2080T>C",
"hgvs_p": "p.Cys694Arg"
}
],
"clinvar_disease": "Autosomal recessive Robinow syndrome,Brachydactyly type B1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"phenotype_combined": "not provided|Autosomal recessive Robinow syndrome|Autosomal recessive Robinow syndrome;Brachydactyly type B1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}