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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: 12-70745852-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=70745852&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 70745852,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002849.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.973C>T",
"hgvs_p": "p.Pro325Ser",
"transcript": "NM_002849.4",
"protein_id": "NP_002840.2",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 657,
"cds_start": 973,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000283228.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002849.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.973C>T",
"hgvs_p": "p.Pro325Ser",
"transcript": "ENST00000283228.7",
"protein_id": "ENSP00000283228.2",
"transcript_support_level": 1,
"aa_start": 325,
"aa_end": null,
"aa_length": 657,
"cds_start": 973,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002849.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000283228.7"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.355C>T",
"hgvs_p": "p.Pro119Ser",
"transcript": "ENST00000378778.5",
"protein_id": "ENSP00000368054.1",
"transcript_support_level": 1,
"aa_start": 119,
"aa_end": null,
"aa_length": 451,
"cds_start": 355,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378778.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.238C>T",
"hgvs_p": "p.Pro80Ser",
"transcript": "ENST00000440835.6",
"protein_id": "ENSP00000391750.2",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 412,
"cds_start": 238,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000440835.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.238C>T",
"hgvs_p": "p.Pro80Ser",
"transcript": "ENST00000549308.5",
"protein_id": "ENSP00000446943.1",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 412,
"cds_start": 238,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549308.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "n.-44C>T",
"hgvs_p": null,
"transcript": "ENST00000551219.5",
"protein_id": "ENSP00000448049.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000551219.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "n.-44C>T",
"hgvs_p": null,
"transcript": "ENST00000551219.5",
"protein_id": "ENSP00000448049.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000551219.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.637C>T",
"hgvs_p": "p.Pro213Ser",
"transcript": "NM_001207015.2",
"protein_id": "NP_001193944.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 545,
"cds_start": 637,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001207015.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.637C>T",
"hgvs_p": "p.Pro213Ser",
"transcript": "ENST00000342084.8",
"protein_id": "ENSP00000339605.4",
"transcript_support_level": 2,
"aa_start": 213,
"aa_end": null,
"aa_length": 545,
"cds_start": 637,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342084.8"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.355C>T",
"hgvs_p": "p.Pro119Ser",
"transcript": "NM_001207016.1",
"protein_id": "NP_001193945.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 451,
"cds_start": 355,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001207016.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.238C>T",
"hgvs_p": "p.Pro80Ser",
"transcript": "NM_130846.3",
"protein_id": "NP_570897.2",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 412,
"cds_start": 238,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130846.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.238C>T",
"hgvs_p": "p.Pro80Ser",
"transcript": "ENST00000550661.1",
"protein_id": "ENSP00000449616.1",
"transcript_support_level": 3,
"aa_start": 80,
"aa_end": null,
"aa_length": 197,
"cds_start": 238,
"cds_end": null,
"cds_length": 596,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000550661.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Pro317Ser",
"transcript": "XM_011538615.3",
"protein_id": "XP_011536917.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 649,
"cds_start": 949,
"cds_end": null,
"cds_length": 1950,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538615.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.973C>T",
"hgvs_p": "p.Pro325Ser",
"transcript": "XM_047429233.1",
"protein_id": "XP_047285189.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 537,
"cds_start": 973,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429233.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Pro174Ser",
"transcript": "XM_047429234.1",
"protein_id": "XP_047285190.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 391,
"cds_start": 520,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429234.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Pro174Ser",
"transcript": "XM_047429235.1",
"protein_id": "XP_047285191.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 386,
"cds_start": 520,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429235.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "n.521C>T",
"hgvs_p": null,
"transcript": "ENST00000548220.1",
"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": "pseudogene",
"feature": "ENST00000548220.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"hgvs_c": "n.653C>T",
"hgvs_p": null,
"transcript": "NR_073474.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_073474.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307941",
"gene_hgnc_id": null,
"hgvs_c": "n.72+26029G>A",
"hgvs_p": null,
"transcript": "ENST00000829948.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000829948.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124902960",
"gene_hgnc_id": null,
"hgvs_c": "n.628+26029G>A",
"hgvs_p": null,
"transcript": "XR_007063361.1",
"protein_id": null,
"transcript_support_level": null,
"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": "XR_007063361.1"
}
],
"gene_symbol": "PTPRR",
"gene_hgnc_id": 9680,
"dbsnp": "rs140514774",
"frequency_reference_population": 0.000039033748,
"hom_count_reference_population": 0,
"allele_count_reference_population": 63,
"gnomad_exomes_af": 0.000041044,
"gnomad_genomes_af": 0.0000197184,
"gnomad_exomes_ac": 60,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3936745524406433,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.209,
"revel_prediction": "Benign",
"alphamissense_score": 0.327,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.993,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002849.4",
"gene_symbol": "PTPRR",
"hgnc_id": 9680,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.973C>T",
"hgvs_p": "p.Pro325Ser"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000829948.1",
"gene_symbol": "ENSG00000307941",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.72+26029G>A",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007063361.1",
"gene_symbol": "LOC124902960",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.628+26029G>A",
"hgvs_p": null
}
],
"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
}