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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: 20-49012058-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=49012058&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ARFGEF2",
"hgnc_id": 15853,
"hgvs_c": "c.3892G>A",
"hgvs_p": "p.Gly1298Ser",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_006420.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 2207,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1382,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.33,
"chr": "20",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " autosomal recessive,ARFGEF2-related disorder,Intellectual disability,Periventricular heterotopia with microcephaly,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.01025998592376709,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1785,
"aa_ref": "G",
"aa_start": 1298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9031,
"cdna_start": 4071,
"cds_end": null,
"cds_length": 5358,
"cds_start": 3892,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_006420.3",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3892G>A",
"hgvs_p": "p.Gly1298Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371917.5",
"protein_coding": true,
"protein_id": "NP_006411.2",
"strand": true,
"transcript": "NM_006420.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1785,
"aa_ref": "G",
"aa_start": 1298,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9031,
"cdna_start": 4071,
"cds_end": null,
"cds_length": 5358,
"cds_start": 3892,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000371917.5",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3892G>A",
"hgvs_p": "p.Gly1298Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006420.3",
"protein_coding": true,
"protein_id": "ENSP00000360985.4",
"strand": true,
"transcript": "ENST00000371917.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1784,
"aa_ref": "G",
"aa_start": 1297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9028,
"cdna_start": 4068,
"cds_end": null,
"cds_length": 5355,
"cds_start": 3889,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_001410846.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3889G>A",
"hgvs_p": "p.Gly1297Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397775.1",
"strand": true,
"transcript": "NM_001410846.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1784,
"aa_ref": "G",
"aa_start": 1297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8828,
"cdna_start": 3889,
"cds_end": null,
"cds_length": 5355,
"cds_start": 3889,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000679436.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3889G>A",
"hgvs_p": "p.Gly1297Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000504888.1",
"strand": true,
"transcript": "ENST00000679436.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1783,
"aa_ref": "G",
"aa_start": 1296,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8973,
"cdna_start": 4013,
"cds_end": null,
"cds_length": 5352,
"cds_start": 3886,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000939861.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3886G>A",
"hgvs_p": "p.Gly1296Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000609920.1",
"strand": true,
"transcript": "ENST00000939861.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1728,
"aa_ref": "G",
"aa_start": 1298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6583,
"cdna_start": 3892,
"cds_end": null,
"cds_length": 5187,
"cds_start": 3892,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000681021.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3892G>A",
"hgvs_p": "p.Gly1298Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000505972.1",
"strand": true,
"transcript": "ENST00000681021.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1705,
"aa_ref": "G",
"aa_start": 1218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8069,
"cdna_start": 3814,
"cds_end": null,
"cds_length": 5118,
"cds_start": 3652,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000963182.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3652G>A",
"hgvs_p": "p.Gly1218Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633241.1",
"strand": true,
"transcript": "ENST00000963182.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1597,
"aa_ref": "G",
"aa_start": 1110,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8876,
"cdna_start": 3916,
"cds_end": null,
"cds_length": 4794,
"cds_start": 3328,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "XM_047439832.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "c.3328G>A",
"hgvs_p": "p.Gly1110Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047295788.1",
"strand": true,
"transcript": "XM_047439832.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 8520,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 34,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000679542.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.3449G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000679542.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4364,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 30,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000680635.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.3449G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000680635.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5206,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 38,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000680871.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.*2720G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505042.1",
"strand": true,
"transcript": "ENST00000680871.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 8731,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 37,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000681399.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.*3569G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506363.1",
"strand": true,
"transcript": "ENST00000681399.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5249,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 38,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000681656.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.*2088G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505638.1",
"strand": true,
"transcript": "ENST00000681656.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5660,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 38,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000681885.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.3892G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505737.1",
"strand": true,
"transcript": "ENST00000681885.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5206,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 38,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000680871.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.*2720G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505042.1",
"strand": true,
"transcript": "ENST00000680871.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 8731,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 37,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000681399.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.*3569G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506363.1",
"strand": true,
"transcript": "ENST00000681399.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5249,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 38,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000681656.1",
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"hgvs_c": "n.*2088G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000505638.1",
"strand": true,
"transcript": "ENST00000681656.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs139037316",
"effect": "missense_variant",
"frequency_reference_population": 0.0013672712,
"gene_hgnc_id": 15853,
"gene_symbol": "ARFGEF2",
"gnomad_exomes_ac": 2028,
"gnomad_exomes_af": 0.00138725,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_ac": 179,
"gnomad_genomes_af": 0.00117547,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 4,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|not provided|ARFGEF2-related disorder|Periventricular heterotopia with microcephaly, autosomal recessive|Intellectual disability",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.91,
"pos": 49012058,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.17,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05000000074505806,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.05,
"transcript": "NM_006420.3"
}
]
}