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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: 2-218383101-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218383101&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 218383101,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000578.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "c.149C>T",
"hgvs_p": "p.Pro50Leu",
"transcript": "NM_000578.4",
"protein_id": "NP_000569.3",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 550,
"cds_start": 149,
"cds_end": null,
"cds_length": 1653,
"cdna_start": 245,
"cdna_end": null,
"cdna_length": 3608,
"mane_select": "ENST00000233202.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "c.149C>T",
"hgvs_p": "p.Pro50Leu",
"transcript": "ENST00000233202.11",
"protein_id": "ENSP00000233202.6",
"transcript_support_level": 1,
"aa_start": 50,
"aa_end": null,
"aa_length": 550,
"cds_start": 149,
"cds_end": null,
"cds_length": 1653,
"cdna_start": 245,
"cdna_end": null,
"cdna_length": 3608,
"mane_select": "NM_000578.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.149C>T",
"hgvs_p": null,
"transcript": "ENST00000354352.9",
"protein_id": "ENSP00000346320.5",
"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": 2136,
"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": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.489C>T",
"hgvs_p": null,
"transcript": "ENST00000468221.5",
"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": 5772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.245C>T",
"hgvs_p": null,
"transcript": "ENST00000494322.5",
"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": 1781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.7+726C>T",
"hgvs_p": null,
"transcript": "ENST00000539932.5",
"protein_id": "ENSP00000443435.2",
"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": 1765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "c.149C>T",
"hgvs_p": "p.Pro50Leu",
"transcript": "XM_047445574.1",
"protein_id": "XP_047301530.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 426,
"cds_start": 149,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 245,
"cdna_end": null,
"cdna_length": 1390,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "c.149C>T",
"hgvs_p": "p.Pro50Leu",
"transcript": "XM_047445575.1",
"protein_id": "XP_047301531.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 297,
"cds_start": 149,
"cds_end": null,
"cds_length": 894,
"cdna_start": 245,
"cdna_end": null,
"cdna_length": 1235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.330C>T",
"hgvs_p": null,
"transcript": "ENST00000465984.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.149C>T",
"hgvs_p": null,
"transcript": "ENST00000473367.5",
"protein_id": "ENSP00000484905.1",
"transcript_support_level": 4,
"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": 624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.231C>T",
"hgvs_p": null,
"transcript": "ENST00000492413.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.97+726C>T",
"hgvs_p": null,
"transcript": "ENST00000469799.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 695,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.97+726C>T",
"hgvs_p": null,
"transcript": "ENST00000471875.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.185+31C>T",
"hgvs_p": null,
"transcript": "ENST00000475225.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.7+726C>T",
"hgvs_p": null,
"transcript": "ENST00000481524.5",
"protein_id": "ENSP00000483970.1",
"transcript_support_level": 4,
"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": 421,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "n.7+726C>T",
"hgvs_p": null,
"transcript": "ENST00000714041.1",
"protein_id": "ENSP00000519332.1",
"transcript_support_level": null,
"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": 1195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "c.-52+726C>T",
"hgvs_p": null,
"transcript": "XM_005246793.5",
"protein_id": "XP_005246850.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 483,
"cds_start": -4,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "c.-52+31C>T",
"hgvs_p": null,
"transcript": "XM_017004766.3",
"protein_id": "XP_016860255.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 483,
"cds_start": -4,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"hgvs_c": "c.-175+726C>T",
"hgvs_p": null,
"transcript": "XM_006712711.5",
"protein_id": "XP_006712774.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 401,
"cds_start": -4,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC11A1",
"gene_hgnc_id": 10907,
"dbsnp": "rs769490777",
"frequency_reference_population": 0.000019213057,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000191611,
"gnomad_genomes_af": 0.0000197122,
"gnomad_exomes_ac": 28,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03242608904838562,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.06800000369548798,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.01,
"revel_prediction": "Benign",
"alphamissense_score": 0.0807,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.821,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.024044606409369,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_000578.4",
"gene_symbol": "SLC11A1",
"hgnc_id": 10907,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.149C>T",
"hgvs_p": "p.Pro50Leu"
}
],
"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
}