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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: 4-25667908-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=25667908&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 25667908,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_006424.3",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile",
"transcript": "NM_006424.3",
"protein_id": "NP_006415.3",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 690,
"cds_start": 552,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000382051.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006424.3"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile",
"transcript": "ENST00000382051.8",
"protein_id": "ENSP00000371483.3",
"transcript_support_level": 1,
"aa_start": 184,
"aa_end": null,
"aa_length": 690,
"cds_start": 552,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006424.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000382051.8"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "ENST00000503434.5",
"protein_id": "ENSP00000423021.1",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503434.5"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "ENST00000504570.5",
"protein_id": "ENSP00000425501.1",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504570.5"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile",
"transcript": "ENST00000872278.1",
"protein_id": "ENSP00000542337.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 690,
"cds_start": 552,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872278.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile",
"transcript": "ENST00000872280.1",
"protein_id": "ENSP00000542339.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 690,
"cds_start": 552,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872280.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile",
"transcript": "ENST00000954978.1",
"protein_id": "ENSP00000625037.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 690,
"cds_start": 552,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954978.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "NM_001177998.2",
"protein_id": "NP_001171469.2",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001177998.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "NM_001177999.2",
"protein_id": "NP_001171470.2",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001177999.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "ENST00000645788.1",
"protein_id": "ENSP00000494094.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000645788.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "ENST00000872279.1",
"protein_id": "ENSP00000542338.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872279.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "ENST00000872282.1",
"protein_id": "ENSP00000542341.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872282.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "ENST00000954979.1",
"protein_id": "ENSP00000625038.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 689,
"cds_start": 549,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954979.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile",
"transcript": "ENST00000954977.1",
"protein_id": "ENSP00000625036.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 671,
"cds_start": 552,
"cds_end": null,
"cds_length": 2016,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954977.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile",
"transcript": "ENST00000872281.1",
"protein_id": "ENSP00000542340.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 660,
"cds_start": 552,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872281.1"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "c.549T>C",
"hgvs_p": "p.Ile183Ile",
"transcript": "ENST00000954976.1",
"protein_id": "ENSP00000625035.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 659,
"cds_start": 549,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954976.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"hgvs_c": "n.570T>C",
"hgvs_p": null,
"transcript": "ENST00000510033.2",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000510033.2"
}
],
"gene_symbol": "SLC34A2",
"gene_hgnc_id": 11020,
"dbsnp": "rs77319279",
"frequency_reference_population": 0.027163636,
"hom_count_reference_population": 788,
"allele_count_reference_population": 43810,
"gnomad_exomes_af": 0.0277051,
"gnomad_genomes_af": 0.021971,
"gnomad_exomes_ac": 40464,
"gnomad_genomes_ac": 3346,
"gnomad_exomes_homalt": 710,
"gnomad_genomes_homalt": 78,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5400000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.122,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_006424.3",
"gene_symbol": "SLC34A2",
"hgnc_id": 11020,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.552T>C",
"hgvs_p": "p.Ile184Ile"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}