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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: 7-157595301-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=157595301&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 157595301,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_001308268.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2433G>A",
"hgvs_p": "p.Pro811Pro",
"transcript": "NM_002847.5",
"protein_id": "NP_002838.2",
"transcript_support_level": null,
"aa_start": 811,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2433,
"cds_end": null,
"cds_length": 3048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000389418.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002847.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2433G>A",
"hgvs_p": "p.Pro811Pro",
"transcript": "ENST00000389418.9",
"protein_id": "ENSP00000374069.4",
"transcript_support_level": 1,
"aa_start": 811,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2433,
"cds_end": null,
"cds_length": 3048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002847.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389418.9"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2382G>A",
"hgvs_p": "p.Pro794Pro",
"transcript": "ENST00000389416.8",
"protein_id": "ENSP00000374067.4",
"transcript_support_level": 1,
"aa_start": 794,
"aa_end": null,
"aa_length": 998,
"cds_start": 2382,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389416.8"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2346G>A",
"hgvs_p": "p.Pro782Pro",
"transcript": "ENST00000389413.7",
"protein_id": "ENSP00000374064.3",
"transcript_support_level": 1,
"aa_start": 782,
"aa_end": null,
"aa_length": 986,
"cds_start": 2346,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389413.7"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2502G>A",
"hgvs_p": "p.Pro834Pro",
"transcript": "NM_001308268.2",
"protein_id": "NP_001295197.1",
"transcript_support_level": null,
"aa_start": 834,
"aa_end": null,
"aa_length": 1038,
"cds_start": 2502,
"cds_end": null,
"cds_length": 3117,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308268.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2382G>A",
"hgvs_p": "p.Pro794Pro",
"transcript": "NM_130842.4",
"protein_id": "NP_570857.2",
"transcript_support_level": null,
"aa_start": 794,
"aa_end": null,
"aa_length": 998,
"cds_start": 2382,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130842.4"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2346G>A",
"hgvs_p": "p.Pro782Pro",
"transcript": "NM_130843.4",
"protein_id": "NP_570858.2",
"transcript_support_level": null,
"aa_start": 782,
"aa_end": null,
"aa_length": 986,
"cds_start": 2346,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130843.4"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2319G>A",
"hgvs_p": "p.Pro773Pro",
"transcript": "NM_001308267.2",
"protein_id": "NP_001295196.1",
"transcript_support_level": null,
"aa_start": 773,
"aa_end": null,
"aa_length": 977,
"cds_start": 2319,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308267.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2319G>A",
"hgvs_p": "p.Pro773Pro",
"transcript": "ENST00000409483.5",
"protein_id": "ENSP00000387114.1",
"transcript_support_level": 2,
"aa_start": 773,
"aa_end": null,
"aa_length": 977,
"cds_start": 2319,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409483.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.237G>A",
"hgvs_p": "p.Pro79Pro",
"transcript": "ENST00000648371.1",
"protein_id": "ENSP00000498058.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 293,
"cds_start": 237,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648371.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2295G>A",
"hgvs_p": "p.Pro765Pro",
"transcript": "XM_047420678.1",
"protein_id": "XP_047276634.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 969,
"cds_start": 2295,
"cds_end": null,
"cds_length": 2910,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420678.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2235G>A",
"hgvs_p": "p.Pro745Pro",
"transcript": "XM_017012475.1",
"protein_id": "XP_016867964.1",
"transcript_support_level": null,
"aa_start": 745,
"aa_end": null,
"aa_length": 949,
"cds_start": 2235,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017012475.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2232G>A",
"hgvs_p": "p.Pro744Pro",
"transcript": "XM_047420679.1",
"protein_id": "XP_047276635.1",
"transcript_support_level": null,
"aa_start": 744,
"aa_end": null,
"aa_length": 948,
"cds_start": 2232,
"cds_end": null,
"cds_length": 2847,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420679.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2433G>A",
"hgvs_p": "p.Pro811Pro",
"transcript": "XM_017012476.2",
"protein_id": "XP_016867965.1",
"transcript_support_level": null,
"aa_start": 811,
"aa_end": null,
"aa_length": 866,
"cds_start": 2433,
"cds_end": null,
"cds_length": 2601,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017012476.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2433G>A",
"hgvs_p": "p.Pro811Pro",
"transcript": "XM_011516446.2",
"protein_id": "XP_011514748.1",
"transcript_support_level": null,
"aa_start": 811,
"aa_end": null,
"aa_length": 834,
"cds_start": 2433,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011516446.2"
}
],
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"dbsnp": "rs139627101",
"frequency_reference_population": 0.0005501184,
"hom_count_reference_population": 5,
"allele_count_reference_population": 888,
"gnomad_exomes_af": 0.000327663,
"gnomad_genomes_af": 0.00268493,
"gnomad_exomes_ac": 479,
"gnomad_genomes_ac": 409,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.354,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001308268.2",
"gene_symbol": "PTPRN2",
"hgnc_id": 9677,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2502G>A",
"hgvs_p": "p.Pro834Pro"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}