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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: 7-84999444-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=84999444&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 84999444,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152754.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met",
"transcript": "NM_001384900.1",
"protein_id": "NP_001371829.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 777,
"cds_start": 2330,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000284136.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001384900.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met",
"transcript": "ENST00000284136.11",
"protein_id": "ENSP00000284136.6",
"transcript_support_level": 5,
"aa_start": 777,
"aa_end": null,
"aa_length": 777,
"cds_start": 2330,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001384900.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000284136.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "n.1456C>T",
"hgvs_p": null,
"transcript": "ENST00000484038.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000484038.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met",
"transcript": "NM_001384901.1",
"protein_id": "NP_001371830.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 777,
"cds_start": 2330,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001384901.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met",
"transcript": "NM_001384902.1",
"protein_id": "NP_001371831.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 777,
"cds_start": 2330,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001384902.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met",
"transcript": "NM_001384903.1",
"protein_id": "NP_001371832.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 777,
"cds_start": 2330,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001384903.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met",
"transcript": "NM_152754.3",
"protein_id": "NP_689967.2",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 777,
"cds_start": 2330,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152754.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met",
"transcript": "ENST00000916323.1",
"protein_id": "ENSP00000586382.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 777,
"cds_start": 2330,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916323.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.1748C>T",
"hgvs_p": "p.Thr583Met",
"transcript": "XM_011515961.3",
"protein_id": "XP_011514263.1",
"transcript_support_level": null,
"aa_start": 583,
"aa_end": null,
"aa_length": 583,
"cds_start": 1748,
"cds_end": null,
"cds_length": 1752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011515961.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"hgvs_c": "c.1748C>T",
"hgvs_p": "p.Thr583Met",
"transcript": "XM_047420049.1",
"protein_id": "XP_047276005.1",
"transcript_support_level": null,
"aa_start": 583,
"aa_end": null,
"aa_length": 583,
"cds_start": 1748,
"cds_end": null,
"cds_length": 1752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420049.1"
}
],
"gene_symbol": "SEMA3D",
"gene_hgnc_id": 10726,
"dbsnp": "rs1171852696",
"frequency_reference_population": 0.000004342168,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000410963,
"gnomad_genomes_af": 0.00000657402,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20894113183021545,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.145,
"revel_prediction": "Benign",
"alphamissense_score": 0.1377,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.688,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_152754.3",
"gene_symbol": "SEMA3D",
"hgnc_id": 10726,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2330C>T",
"hgvs_p": "p.Thr777Met"
}
],
"clinvar_disease": "SEMA3D-related disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "SEMA3D-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}