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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: 14-88473673-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=88473673&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 88473673,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_007039.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn",
"transcript": "NM_007039.4",
"protein_id": "NP_008970.2",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2641,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000556564.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007039.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn",
"transcript": "ENST00000556564.6",
"protein_id": "ENSP00000452414.1",
"transcript_support_level": 1,
"aa_start": 881,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2641,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007039.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000556564.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn",
"transcript": "ENST00000328736.7",
"protein_id": "ENSP00000330276.3",
"transcript_support_level": 1,
"aa_start": 881,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2641,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000328736.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.*2578G>A",
"hgvs_p": null,
"transcript": "ENST00000536337.5",
"protein_id": "ENSP00000443951.1",
"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": "ENST00000536337.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.2754G>A",
"hgvs_p": null,
"transcript": "ENST00000554270.5",
"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": "retained_intron",
"feature": "ENST00000554270.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.*2578G>A",
"hgvs_p": null,
"transcript": "ENST00000536337.5",
"protein_id": "ENSP00000443951.1",
"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": "ENST00000536337.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn",
"transcript": "ENST00000872152.1",
"protein_id": "ENSP00000542211.1",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2641,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872152.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn",
"transcript": "ENST00000940832.1",
"protein_id": "ENSP00000610891.1",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2641,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940832.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2545G>A",
"hgvs_p": "p.Asp849Asn",
"transcript": "ENST00000940831.1",
"protein_id": "ENSP00000610890.1",
"transcript_support_level": null,
"aa_start": 849,
"aa_end": null,
"aa_length": 1142,
"cds_start": 2545,
"cds_end": null,
"cds_length": 3429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940831.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn",
"transcript": "XM_005267287.4",
"protein_id": "XP_005267344.1",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2641,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005267287.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn",
"transcript": "XM_011536367.4",
"protein_id": "XP_011534669.1",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2641,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536367.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2272G>A",
"hgvs_p": "p.Asp758Asn",
"transcript": "XM_011536368.3",
"protein_id": "XP_011534670.1",
"transcript_support_level": null,
"aa_start": 758,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2272,
"cds_end": null,
"cds_length": 3156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536368.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "c.2029G>A",
"hgvs_p": "p.Asp677Asn",
"transcript": "XM_017020939.2",
"protein_id": "XP_016876428.1",
"transcript_support_level": null,
"aa_start": 677,
"aa_end": null,
"aa_length": 970,
"cds_start": 2029,
"cds_end": null,
"cds_length": 2913,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017020939.2"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"hgvs_c": "n.260G>A",
"hgvs_p": null,
"transcript": "ENST00000557249.1",
"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": "ENST00000557249.1"
}
],
"gene_symbol": "PTPN21",
"gene_hgnc_id": 9651,
"dbsnp": "rs1595342164",
"frequency_reference_population": 0.0000065797267,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657973,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8039335012435913,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.279,
"revel_prediction": "Benign",
"alphamissense_score": 0.4474,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.62,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_007039.4",
"gene_symbol": "PTPN21",
"hgnc_id": 9651,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2641G>A",
"hgvs_p": "p.Asp881Asn"
}
],
"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
}