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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: 2-236049178-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=236049178&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 236049178,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001436125.1",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.2011G>A",
"hgvs_p": "p.Val671Ile",
"transcript": "NM_001037131.3",
"protein_id": "NP_001032208.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 857,
"cds_start": 2011,
"cds_end": null,
"cds_length": 2574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000304032.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001037131.3"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.2011G>A",
"hgvs_p": "p.Val671Ile",
"transcript": "ENST00000304032.13",
"protein_id": "ENSP00000307634.7",
"transcript_support_level": 5,
"aa_start": 671,
"aa_end": null,
"aa_length": 857,
"cds_start": 2011,
"cds_end": null,
"cds_length": 2574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001037131.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000304032.13"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.1852G>A",
"hgvs_p": "p.Val618Ile",
"transcript": "ENST00000336665.9",
"protein_id": "ENSP00000338378.5",
"transcript_support_level": 1,
"aa_start": 618,
"aa_end": null,
"aa_length": 804,
"cds_start": 1852,
"cds_end": null,
"cds_length": 2415,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336665.9"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.2806G>A",
"hgvs_p": "p.Val936Ile",
"transcript": "NM_001436125.1",
"protein_id": "NP_001423054.1",
"transcript_support_level": null,
"aa_start": 936,
"aa_end": null,
"aa_length": 1122,
"cds_start": 2806,
"cds_end": null,
"cds_length": 3369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436125.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.2647G>A",
"hgvs_p": "p.Val883Ile",
"transcript": "NM_001436126.1",
"protein_id": "NP_001423055.1",
"transcript_support_level": null,
"aa_start": 883,
"aa_end": null,
"aa_length": 1069,
"cds_start": 2647,
"cds_end": null,
"cds_length": 3210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436126.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.2647G>A",
"hgvs_p": "p.Val883Ile",
"transcript": "ENST00000409538.5",
"protein_id": "ENSP00000386897.1",
"transcript_support_level": 5,
"aa_start": 883,
"aa_end": null,
"aa_length": 1069,
"cds_start": 2647,
"cds_end": null,
"cds_length": 3210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409538.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.2098G>A",
"hgvs_p": "p.Val700Ile",
"transcript": "ENST00000635100.2",
"protein_id": "ENSP00000489496.2",
"transcript_support_level": 5,
"aa_start": 700,
"aa_end": null,
"aa_length": 886,
"cds_start": 2098,
"cds_end": null,
"cds_length": 2661,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635100.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.2086G>A",
"hgvs_p": "p.Val696Ile",
"transcript": "ENST00000448025.6",
"protein_id": "ENSP00000403482.2",
"transcript_support_level": 5,
"aa_start": 696,
"aa_end": null,
"aa_length": 882,
"cds_start": 2086,
"cds_end": null,
"cds_length": 2649,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000448025.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.1927G>A",
"hgvs_p": "p.Val643Ile",
"transcript": "ENST00000418654.2",
"protein_id": "ENSP00000393838.2",
"transcript_support_level": 3,
"aa_start": 643,
"aa_end": null,
"aa_length": 829,
"cds_start": 1927,
"cds_end": null,
"cds_length": 2490,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000418654.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.1864G>A",
"hgvs_p": "p.Val622Ile",
"transcript": "ENST00000699337.1",
"protein_id": "ENSP00000514311.1",
"transcript_support_level": null,
"aa_start": 622,
"aa_end": null,
"aa_length": 808,
"cds_start": 1864,
"cds_end": null,
"cds_length": 2427,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000699337.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "c.1852G>A",
"hgvs_p": "p.Val618Ile",
"transcript": "NM_014914.5",
"protein_id": "NP_055729.2",
"transcript_support_level": null,
"aa_start": 618,
"aa_end": null,
"aa_length": 804,
"cds_start": 1852,
"cds_end": null,
"cds_length": 2415,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014914.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "n.215G>A",
"hgvs_p": null,
"transcript": "ENST00000453371.2",
"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": "ENST00000453371.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "n.350G>A",
"hgvs_p": null,
"transcript": "ENST00000466575.5",
"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": "retained_intron",
"feature": "ENST00000466575.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"hgvs_c": "n.211G>A",
"hgvs_p": null,
"transcript": "ENST00000482882.1",
"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": "retained_intron",
"feature": "ENST00000482882.1"
}
],
"gene_symbol": "AGAP1",
"gene_hgnc_id": 16922,
"dbsnp": "rs2034648",
"frequency_reference_population": 0.5561416,
"hom_count_reference_population": 257386,
"allele_count_reference_population": 897597,
"gnomad_exomes_af": 0.546557,
"gnomad_genomes_af": 0.64823,
"gnomad_exomes_ac": 798974,
"gnomad_genomes_ac": 98623,
"gnomad_exomes_homalt": 223516,
"gnomad_genomes_homalt": 33870,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 6.932896212674677e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.041,
"revel_prediction": "Benign",
"alphamissense_score": 0.0645,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.638,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001436125.1",
"gene_symbol": "AGAP1",
"hgnc_id": 16922,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2806G>A",
"hgvs_p": "p.Val936Ile"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}