← Back to variant description
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: 2-196841294-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=196841294&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 196841294,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_024989.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2709T>C",
"hgvs_p": "p.Tyr903Tyr",
"transcript": "NM_024989.4",
"protein_id": "NP_079265.2",
"transcript_support_level": null,
"aa_start": 903,
"aa_end": null,
"aa_length": 922,
"cds_start": 2709,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000354764.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024989.4"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2709T>C",
"hgvs_p": "p.Tyr903Tyr",
"transcript": "ENST00000354764.9",
"protein_id": "ENSP00000346809.3",
"transcript_support_level": 1,
"aa_start": 903,
"aa_end": null,
"aa_length": 922,
"cds_start": 2709,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024989.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000354764.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*2640T>C",
"hgvs_p": null,
"transcript": "ENST00000423035.5",
"protein_id": "ENSP00000415405.1",
"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": "ENST00000423035.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*2640T>C",
"hgvs_p": null,
"transcript": "ENST00000423035.5",
"protein_id": "ENSP00000415405.1",
"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": "ENST00000423035.5"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2802T>C",
"hgvs_p": "p.Tyr934Tyr",
"transcript": "ENST00000961224.1",
"protein_id": "ENSP00000631283.1",
"transcript_support_level": null,
"aa_start": 934,
"aa_end": null,
"aa_length": 953,
"cds_start": 2802,
"cds_end": null,
"cds_length": 2862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961224.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2571T>C",
"hgvs_p": "p.Tyr857Tyr",
"transcript": "ENST00000911521.1",
"protein_id": "ENSP00000581580.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 876,
"cds_start": 2571,
"cds_end": null,
"cds_length": 2631,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911521.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2547T>C",
"hgvs_p": "p.Tyr849Tyr",
"transcript": "ENST00000862441.1",
"protein_id": "ENSP00000532500.1",
"transcript_support_level": null,
"aa_start": 849,
"aa_end": null,
"aa_length": 868,
"cds_start": 2547,
"cds_end": null,
"cds_length": 2607,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862441.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2187T>C",
"hgvs_p": "p.Tyr729Tyr",
"transcript": "NM_001321099.2",
"protein_id": "NP_001308028.1",
"transcript_support_level": null,
"aa_start": 729,
"aa_end": null,
"aa_length": 748,
"cds_start": 2187,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321099.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1542T>C",
"hgvs_p": "p.Tyr514Tyr",
"transcript": "NM_001321100.2",
"protein_id": "NP_001308029.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 533,
"cds_start": 1542,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321100.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.420T>C",
"hgvs_p": "p.Tyr140Tyr",
"transcript": "ENST00000422444.1",
"protein_id": "ENSP00000390555.1",
"transcript_support_level": 2,
"aa_start": 140,
"aa_end": null,
"aa_length": 159,
"cds_start": 420,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000422444.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2187T>C",
"hgvs_p": "p.Tyr729Tyr",
"transcript": "XM_017004992.1",
"protein_id": "XP_016860481.1",
"transcript_support_level": null,
"aa_start": 729,
"aa_end": null,
"aa_length": 748,
"cds_start": 2187,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004992.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2187T>C",
"hgvs_p": "p.Tyr729Tyr",
"transcript": "XM_017004993.2",
"protein_id": "XP_016860482.1",
"transcript_support_level": null,
"aa_start": 729,
"aa_end": null,
"aa_length": 748,
"cds_start": 2187,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004993.2"
},
{
"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": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.105+1427T>C",
"hgvs_p": null,
"transcript": "ENST00000459896.5",
"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": "ENST00000459896.5"
},
{
"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": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*45T>C",
"hgvs_p": null,
"transcript": "ENST00000470179.5",
"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": "retained_intron",
"feature": "ENST00000470179.5"
}
],
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"dbsnp": "rs750068372",
"frequency_reference_population": 0.0000034207026,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.0000034207,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5899999737739563,
"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": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.579,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_024989.4",
"gene_symbol": "PGAP1",
"hgnc_id": 25712,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2709T>C",
"hgvs_p": "p.Tyr903Tyr"
}
],
"clinvar_disease": " autosomal recessive 42,Intellectual disability",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Intellectual disability, autosomal recessive 42",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}