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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: 9-137139508-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=137139508&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 137139508,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_007327.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "NM_007327.4",
"protein_id": "NP_015566.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 938,
"cds_start": 22,
"cds_end": null,
"cds_length": 2817,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4379,
"mane_select": "ENST00000371561.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "ENST00000371561.8",
"protein_id": "ENSP00000360616.3",
"transcript_support_level": 1,
"aa_start": 8,
"aa_end": null,
"aa_length": 938,
"cds_start": 22,
"cds_end": null,
"cds_length": 2817,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4379,
"mane_select": "NM_007327.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "ENST00000371553.8",
"protein_id": "ENSP00000360608.3",
"transcript_support_level": 1,
"aa_start": 8,
"aa_end": null,
"aa_length": 943,
"cds_start": 22,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "ENST00000371560.5",
"protein_id": "ENSP00000360615.3",
"transcript_support_level": 1,
"aa_start": 8,
"aa_end": null,
"aa_length": 906,
"cds_start": 22,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 1163,
"cdna_end": null,
"cdna_length": 4775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "ENST00000371559.8",
"protein_id": "ENSP00000360614.4",
"transcript_support_level": 1,
"aa_start": 8,
"aa_end": null,
"aa_length": 885,
"cds_start": 22,
"cds_end": null,
"cds_length": 2658,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 3577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "n.22A>C",
"hgvs_p": null,
"transcript": "ENST00000350902.9",
"protein_id": "ENSP00000316915.9",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "n.99A>C",
"hgvs_p": null,
"transcript": "ENST00000471122.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4184,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "NM_001437330.1",
"protein_id": "NP_001424259.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 959,
"cds_start": 22,
"cds_end": null,
"cds_length": 2880,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "ENST00000371546.8",
"protein_id": "ENSP00000360601.4",
"transcript_support_level": 5,
"aa_start": 8,
"aa_end": null,
"aa_length": 959,
"cds_start": 22,
"cds_end": null,
"cds_length": 2880,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 4114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "NM_001185090.2",
"protein_id": "NP_001172019.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 943,
"cds_start": 22,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "NM_001437331.1",
"protein_id": "NP_001424260.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 922,
"cds_start": 22,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4331,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "ENST00000371555.8",
"protein_id": "ENSP00000360610.4",
"transcript_support_level": 5,
"aa_start": 8,
"aa_end": null,
"aa_length": 922,
"cds_start": 22,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 4003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "NM_001185091.2",
"protein_id": "NP_001172020.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 906,
"cds_start": 22,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 3968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "NM_021569.4",
"protein_id": "NP_067544.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 901,
"cds_start": 22,
"cds_end": null,
"cds_length": 2706,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "ENST00000371550.8",
"protein_id": "ENSP00000360605.4",
"transcript_support_level": 5,
"aa_start": 8,
"aa_end": null,
"aa_length": 901,
"cds_start": 22,
"cds_end": null,
"cds_length": 2706,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 3940,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "NM_000832.7",
"protein_id": "NP_000823.4",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 885,
"cds_start": 22,
"cds_end": null,
"cds_length": 2658,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 3905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "XM_005266071.4",
"protein_id": "XP_005266128.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 922,
"cds_start": 22,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro",
"transcript": "XM_011518583.3",
"protein_id": "XP_011516885.1",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 892,
"cds_start": 22,
"cds_end": null,
"cds_length": 2679,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 4031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GRIN1",
"gene_hgnc_id": 4584,
"dbsnp": "rs768572879",
"frequency_reference_population": 0.000015202273,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000152023,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27381229400634766,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.067,
"revel_prediction": "Benign",
"alphamissense_score": 0.1204,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.351,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6_Very_Strong",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "NM_007327.4",
"gene_symbol": "GRIN1",
"hgnc_id": 4584,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.22A>C",
"hgvs_p": "p.Thr8Pro"
}
],
"clinvar_disease": " autosomal dominant,Intellectual disability,Neurodevelopmental disorder with or without hyperkinetic movements and seizures",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "Intellectual disability|Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}