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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: 10-103601838-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=103601838&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 103601838,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001394015.1",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.3380A>G",
"hgvs_p": "p.Asn1127Ser",
"transcript": "NM_001394015.1",
"protein_id": "NP_001380944.1",
"transcript_support_level": null,
"aa_start": 1127,
"aa_end": null,
"aa_length": 1133,
"cds_start": 3380,
"cds_end": null,
"cds_length": 3402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000369774.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394015.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.3380A>G",
"hgvs_p": "p.Asn1127Ser",
"transcript": "ENST00000369774.9",
"protein_id": "ENSP00000358789.4",
"transcript_support_level": 5,
"aa_start": 1127,
"aa_end": null,
"aa_length": 1133,
"cds_start": 3380,
"cds_end": null,
"cds_length": 3402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001394015.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369774.9"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.3296A>G",
"hgvs_p": "p.Asn1099Ser",
"transcript": "ENST00000355946.7",
"protein_id": "ENSP00000348215.2",
"transcript_support_level": 1,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1105,
"cds_start": 3296,
"cds_end": null,
"cds_length": 3318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355946.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "n.3186A>G",
"hgvs_p": null,
"transcript": "ENST00000315994.6",
"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": "ENST00000315994.6"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.3296A>G",
"hgvs_p": "p.Asn1099Ser",
"transcript": "NM_014631.3",
"protein_id": "NP_055446.2",
"transcript_support_level": null,
"aa_start": 1099,
"aa_end": null,
"aa_length": 1105,
"cds_start": 3296,
"cds_end": null,
"cds_length": 3318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014631.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.3023A>G",
"hgvs_p": "p.Asn1008Ser",
"transcript": "NM_001365079.1",
"protein_id": "NP_001352008.1",
"transcript_support_level": null,
"aa_start": 1008,
"aa_end": null,
"aa_length": 1014,
"cds_start": 3023,
"cds_end": null,
"cds_length": 3045,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365079.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.3011A>G",
"hgvs_p": "p.Asn1004Ser",
"transcript": "NM_001394016.1",
"protein_id": "NP_001380945.1",
"transcript_support_level": null,
"aa_start": 1004,
"aa_end": null,
"aa_length": 1010,
"cds_start": 3011,
"cds_end": null,
"cds_length": 3033,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394016.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.2981A>G",
"hgvs_p": "p.Asn994Ser",
"transcript": "NM_001394017.1",
"protein_id": "NP_001380946.1",
"transcript_support_level": null,
"aa_start": 994,
"aa_end": null,
"aa_length": 1000,
"cds_start": 2981,
"cds_end": null,
"cds_length": 3003,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394017.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.2966A>G",
"hgvs_p": "p.Asn989Ser",
"transcript": "NM_001394018.1",
"protein_id": "NP_001380947.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 995,
"cds_start": 2966,
"cds_end": null,
"cds_length": 2988,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394018.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.2927A>G",
"hgvs_p": "p.Asn976Ser",
"transcript": "NM_001394019.1",
"protein_id": "NP_001380948.1",
"transcript_support_level": null,
"aa_start": 976,
"aa_end": null,
"aa_length": 982,
"cds_start": 2927,
"cds_end": null,
"cds_length": 2949,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394019.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.2885A>G",
"hgvs_p": "p.Asn962Ser",
"transcript": "NM_001394020.1",
"protein_id": "NP_001380949.1",
"transcript_support_level": null,
"aa_start": 962,
"aa_end": null,
"aa_length": 968,
"cds_start": 2885,
"cds_end": null,
"cds_length": 2907,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394020.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.2882A>G",
"hgvs_p": "p.Asn961Ser",
"transcript": "NM_001394021.1",
"protein_id": "NP_001380950.1",
"transcript_support_level": null,
"aa_start": 961,
"aa_end": null,
"aa_length": 967,
"cds_start": 2882,
"cds_end": null,
"cds_length": 2904,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394021.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.2801A>G",
"hgvs_p": "p.Asn934Ser",
"transcript": "NM_001394022.1",
"protein_id": "NP_001380951.1",
"transcript_support_level": null,
"aa_start": 934,
"aa_end": null,
"aa_length": 940,
"cds_start": 2801,
"cds_end": null,
"cds_length": 2823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394022.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "c.2801A>G",
"hgvs_p": "p.Asn934Ser",
"transcript": "NM_001394023.1",
"protein_id": "NP_001380952.1",
"transcript_support_level": null,
"aa_start": 934,
"aa_end": null,
"aa_length": 940,
"cds_start": 2801,
"cds_end": null,
"cds_length": 2823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394023.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "n.2976A>G",
"hgvs_p": null,
"transcript": "ENST00000420222.2",
"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": "pseudogene",
"feature": "ENST00000420222.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"hgvs_c": "n.3192A>G",
"hgvs_p": null,
"transcript": "ENST00000692756.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000692756.1"
}
],
"gene_symbol": "SH3PXD2A",
"gene_hgnc_id": 23664,
"dbsnp": "rs951329846",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9212096929550171,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.317,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2519,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001394015.1",
"gene_symbol": "SH3PXD2A",
"hgnc_id": 23664,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3380A>G",
"hgvs_p": "p.Asn1127Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}