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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: 7-100631032-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=100631032&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 100631032,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000223051.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.1127C>A",
"hgvs_p": "p.Ala376Asp",
"transcript": "NM_003227.4",
"protein_id": "NP_003218.2",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 801,
"cds_start": 1127,
"cds_end": null,
"cds_length": 2406,
"cdna_start": 1170,
"cdna_end": null,
"cdna_length": 2886,
"mane_select": "ENST00000223051.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.1127C>A",
"hgvs_p": "p.Ala376Asp",
"transcript": "ENST00000223051.8",
"protein_id": "ENSP00000223051.3",
"transcript_support_level": 1,
"aa_start": 376,
"aa_end": null,
"aa_length": 801,
"cds_start": 1127,
"cds_end": null,
"cds_length": 2406,
"cdna_start": 1170,
"cdna_end": null,
"cdna_length": 2886,
"mane_select": "NM_003227.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.1127C>A",
"hgvs_p": "p.Ala376Asp",
"transcript": "ENST00000462107.1",
"protein_id": "ENSP00000420525.1",
"transcript_support_level": 5,
"aa_start": 376,
"aa_end": null,
"aa_length": 801,
"cds_start": 1127,
"cds_end": null,
"cds_length": 2406,
"cdna_start": 1415,
"cdna_end": null,
"cdna_length": 3131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.614C>A",
"hgvs_p": "p.Ala205Asp",
"transcript": "NM_001206855.3",
"protein_id": "NP_001193784.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 630,
"cds_start": 614,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 748,
"cdna_end": null,
"cdna_length": 2464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.870C>A",
"hgvs_p": "p.Gly290Gly",
"transcript": "ENST00000431692.5",
"protein_id": "ENSP00000413905.1",
"transcript_support_level": 5,
"aa_start": 290,
"aa_end": null,
"aa_length": 355,
"cds_start": 870,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 911,
"cdna_end": null,
"cdna_length": 2631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.111C>A",
"hgvs_p": null,
"transcript": "ENST00000462090.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 1844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.875C>A",
"hgvs_p": null,
"transcript": "ENST00000465294.5",
"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": 2763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.320C>A",
"hgvs_p": null,
"transcript": "ENST00000473374.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.581C>A",
"hgvs_p": null,
"transcript": "ENST00000473571.1",
"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": 628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.276C>A",
"hgvs_p": null,
"transcript": "ENST00000473963.1",
"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": 771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.748C>A",
"hgvs_p": null,
"transcript": "ENST00000476304.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 2421,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.478C>A",
"hgvs_p": null,
"transcript": "ENST00000490084.5",
"protein_id": "ENSP00000418942.1",
"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": 2196,
"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": "LOC124901709",
"gene_hgnc_id": null,
"hgvs_c": "n.434-124G>T",
"hgvs_p": null,
"transcript": "XR_007060454.1",
"protein_id": null,
"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": 683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"dbsnp": "rs41303495",
"frequency_reference_population": 0.004697625,
"hom_count_reference_population": 29,
"allele_count_reference_population": 7480,
"gnomad_exomes_af": 0.00480358,
"gnomad_genomes_af": 0.00369602,
"gnomad_exomes_ac": 6917,
"gnomad_genomes_ac": 563,
"gnomad_exomes_homalt": 20,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008852779865264893,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.199,
"revel_prediction": "Benign",
"alphamissense_score": 0.7833,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.536,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000223051.8",
"gene_symbol": "TFR2",
"hgnc_id": 11762,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1127C>A",
"hgvs_p": "p.Ala376Asp"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007060454.1",
"gene_symbol": "LOC124901709",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.434-124G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Hemochromatosis type 3,Hereditary hemochromatosis,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not provided|Hereditary hemochromatosis|Hemochromatosis type 3",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}