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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: 1-31918995-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=31918995&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 31918995,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_080391.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "NM_080391.4",
"protein_id": "NP_536316.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 167,
"cds_start": 71,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000647444.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_080391.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "ENST00000647444.2",
"protein_id": "ENSP00000493688.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 167,
"cds_start": 71,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_080391.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647444.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "ENST00000602725.5",
"protein_id": "ENSP00000473259.1",
"transcript_support_level": 1,
"aa_start": 24,
"aa_end": null,
"aa_length": 167,
"cds_start": 71,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602725.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "NM_001369859.1",
"protein_id": "NP_001356788.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 167,
"cds_start": 71,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001369859.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "NM_001369860.1",
"protein_id": "NP_001356789.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 167,
"cds_start": 71,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001369860.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "ENST00000649841.1",
"protein_id": "ENSP00000497092.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 167,
"cds_start": 71,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649841.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "NM_001195100.2",
"protein_id": "NP_001182029.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 142,
"cds_start": 71,
"cds_end": null,
"cds_length": 429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001195100.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "ENST00000602683.5",
"protein_id": "ENSP00000473490.1",
"transcript_support_level": 2,
"aa_start": 24,
"aa_end": null,
"aa_length": 142,
"cds_start": 71,
"cds_end": null,
"cds_length": 429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000602683.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "NM_001195101.2",
"protein_id": "NP_001182030.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 136,
"cds_start": 71,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001195101.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "NM_001369858.1",
"protein_id": "NP_001356787.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 136,
"cds_start": 71,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001369858.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "ENST00000457805.6",
"protein_id": "ENSP00000409260.2",
"transcript_support_level": 2,
"aa_start": 24,
"aa_end": null,
"aa_length": 136,
"cds_start": 71,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457805.6"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "ENST00000470404.5",
"protein_id": "ENSP00000435941.1",
"transcript_support_level": 3,
"aa_start": 24,
"aa_end": null,
"aa_length": 73,
"cds_start": 71,
"cds_end": null,
"cds_length": 222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000470404.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "ENST00000468531.1",
"protein_id": "ENSP00000437251.1",
"transcript_support_level": 3,
"aa_start": 24,
"aa_end": null,
"aa_length": 62,
"cds_start": 71,
"cds_end": null,
"cds_length": 189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468531.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "n.178A>G",
"hgvs_p": null,
"transcript": "ENST00000484483.1",
"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": "ENST00000484483.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "n.71A>G",
"hgvs_p": null,
"transcript": "ENST00000528253.3",
"protein_id": "ENSP00000433800.1",
"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": "ENST00000528253.3"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "n.71A>G",
"hgvs_p": null,
"transcript": "ENST00000532001.6",
"protein_id": "ENSP00000433050.1",
"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": "ENST00000532001.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000269967",
"gene_hgnc_id": null,
"hgvs_c": "n.485+2362A>G",
"hgvs_p": null,
"transcript": "ENST00000602889.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000602889.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "c.*5A>G",
"hgvs_p": null,
"transcript": "ENST00000534796.5",
"protein_id": "ENSP00000433375.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 21,
"cds_start": null,
"cds_end": null,
"cds_length": 66,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000534796.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "n.*234A>G",
"hgvs_p": null,
"transcript": "ENST00000524384.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000524384.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "n.*135A>G",
"hgvs_p": null,
"transcript": "ENST00000526960.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000526960.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "n.*249A>G",
"hgvs_p": null,
"transcript": "ENST00000528840.1",
"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": "ENST00000528840.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"hgvs_c": "n.*99A>G",
"hgvs_p": null,
"transcript": "ENST00000532289.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000532289.1"
}
],
"gene_symbol": "PTP4A2",
"gene_hgnc_id": 9635,
"dbsnp": "rs532970471",
"frequency_reference_population": 0.0000062512736,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000621755,
"gnomad_genomes_af": 0.00000657212,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6424489617347717,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.538,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0924,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.945,
"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": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_080391.4",
"gene_symbol": "PTP4A2",
"hgnc_id": 9635,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000602889.1",
"gene_symbol": "ENSG00000269967",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.485+2362A>G",
"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
}