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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: 5-131431212-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=131431212&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 131431212,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001164386.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4112G>A",
"hgvs_p": "p.Ser1371Asn",
"transcript": "NM_016340.6",
"protein_id": "NP_057424.3",
"transcript_support_level": null,
"aa_start": 1371,
"aa_end": null,
"aa_length": 1601,
"cds_start": 4112,
"cds_end": null,
"cds_length": 4806,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000509018.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016340.6"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4112G>A",
"hgvs_p": "p.Ser1371Asn",
"transcript": "ENST00000509018.6",
"protein_id": "ENSP00000421684.1",
"transcript_support_level": 1,
"aa_start": 1371,
"aa_end": null,
"aa_length": 1601,
"cds_start": 4112,
"cds_end": null,
"cds_length": 4806,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016340.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000509018.6"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000273217",
"gene_hgnc_id": null,
"hgvs_c": "c.4262G>A",
"hgvs_p": "p.Ser1421Asn",
"transcript": "ENST00000514667.1",
"protein_id": "ENSP00000426948.1",
"transcript_support_level": 2,
"aa_start": 1421,
"aa_end": null,
"aa_length": 1651,
"cds_start": 4262,
"cds_end": null,
"cds_length": 4956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514667.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4136G>A",
"hgvs_p": "p.Ser1379Asn",
"transcript": "ENST00000296859.10",
"protein_id": "ENSP00000296859.6",
"transcript_support_level": 1,
"aa_start": 1379,
"aa_end": null,
"aa_length": 1609,
"cds_start": 4136,
"cds_end": null,
"cds_length": 4830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296859.10"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4151G>A",
"hgvs_p": "p.Ser1384Asn",
"transcript": "ENST00000507093.5",
"protein_id": "ENSP00000426081.2",
"transcript_support_level": 1,
"aa_start": 1384,
"aa_end": null,
"aa_length": 1509,
"cds_start": 4151,
"cds_end": null,
"cds_length": 4530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507093.5"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4136G>A",
"hgvs_p": "p.Ser1379Asn",
"transcript": "ENST00000627212.2",
"protein_id": "ENSP00000487439.1",
"transcript_support_level": 1,
"aa_start": 1379,
"aa_end": null,
"aa_length": 1504,
"cds_start": 4136,
"cds_end": null,
"cds_length": 4515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000627212.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "n.1610G>A",
"hgvs_p": null,
"transcript": "ENST00000512611.5",
"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": "retained_intron",
"feature": "ENST00000512611.5"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4136G>A",
"hgvs_p": "p.Ser1379Asn",
"transcript": "NM_001164386.2",
"protein_id": "NP_001157858.1",
"transcript_support_level": null,
"aa_start": 1379,
"aa_end": null,
"aa_length": 1609,
"cds_start": 4136,
"cds_end": null,
"cds_length": 4830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164386.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4052G>A",
"hgvs_p": "p.Ser1351Asn",
"transcript": "ENST00000952737.1",
"protein_id": "ENSP00000622796.1",
"transcript_support_level": null,
"aa_start": 1351,
"aa_end": null,
"aa_length": 1581,
"cds_start": 4052,
"cds_end": null,
"cds_length": 4746,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952737.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4028G>A",
"hgvs_p": "p.Ser1343Asn",
"transcript": "ENST00000934140.1",
"protein_id": "ENSP00000604199.1",
"transcript_support_level": null,
"aa_start": 1343,
"aa_end": null,
"aa_length": 1573,
"cds_start": 4028,
"cds_end": null,
"cds_length": 4722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934140.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4151G>A",
"hgvs_p": "p.Ser1384Asn",
"transcript": "NM_001164387.2",
"protein_id": "NP_001157859.1",
"transcript_support_level": null,
"aa_start": 1384,
"aa_end": null,
"aa_length": 1509,
"cds_start": 4151,
"cds_end": null,
"cds_length": 4530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164387.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4136G>A",
"hgvs_p": "p.Ser1379Asn",
"transcript": "NM_001164388.2",
"protein_id": "NP_001157860.1",
"transcript_support_level": null,
"aa_start": 1379,
"aa_end": null,
"aa_length": 1504,
"cds_start": 4136,
"cds_end": null,
"cds_length": 4515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164388.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.4112G>A",
"hgvs_p": "p.Ser1371Asn",
"transcript": "ENST00000952736.1",
"protein_id": "ENSP00000622795.1",
"transcript_support_level": null,
"aa_start": 1371,
"aa_end": null,
"aa_length": 1496,
"cds_start": 4112,
"cds_end": null,
"cds_length": 4491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952736.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"hgvs_c": "c.3110G>A",
"hgvs_p": "p.Ser1037Asn",
"transcript": "ENST00000671916.1",
"protein_id": "ENSP00000500379.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 1267,
"cds_start": 3110,
"cds_end": null,
"cds_length": 3804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000671916.1"
}
],
"gene_symbol": "RAPGEF6",
"gene_hgnc_id": 20655,
"dbsnp": "rs150501049",
"frequency_reference_population": 0.0000371703,
"hom_count_reference_population": 0,
"allele_count_reference_population": 60,
"gnomad_exomes_af": 0.0000383066,
"gnomad_genomes_af": 0.0000262633,
"gnomad_exomes_ac": 56,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02977094054222107,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.103,
"revel_prediction": "Benign",
"alphamissense_score": 0.1004,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.685,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001164386.2",
"gene_symbol": "RAPGEF6",
"hgnc_id": 20655,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.4136G>A",
"hgvs_p": "p.Ser1379Asn"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000514667.1",
"gene_symbol": "ENSG00000273217",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.4262G>A",
"hgvs_p": "p.Ser1421Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}