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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: 11-63643495-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=63643495&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 63643495,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000398868.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Val238Met",
"transcript": "NM_015459.5",
"protein_id": "NP_056274.3",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 541,
"cds_start": 712,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 753,
"cdna_end": null,
"cdna_length": 6899,
"mane_select": "ENST00000398868.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Val238Met",
"transcript": "ENST00000398868.8",
"protein_id": "ENSP00000381844.3",
"transcript_support_level": 1,
"aa_start": 238,
"aa_end": null,
"aa_length": 541,
"cds_start": 712,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 753,
"cdna_end": null,
"cdna_length": 6899,
"mane_select": "NM_015459.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.661G>A",
"hgvs_p": "p.Val221Met",
"transcript": "NM_001440716.1",
"protein_id": "NP_001427645.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 524,
"cds_start": 661,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 6848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.658G>A",
"hgvs_p": "p.Val220Met",
"transcript": "NM_001290048.2",
"protein_id": "NP_001276977.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 523,
"cds_start": 658,
"cds_end": null,
"cds_length": 1572,
"cdna_start": 1005,
"cdna_end": null,
"cdna_length": 7151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.658G>A",
"hgvs_p": "p.Val220Met",
"transcript": "ENST00000538786.1",
"protein_id": "ENSP00000437593.1",
"transcript_support_level": 2,
"aa_start": 220,
"aa_end": null,
"aa_length": 523,
"cds_start": 658,
"cds_end": null,
"cds_length": 1572,
"cdna_start": 940,
"cdna_end": null,
"cdna_length": 1920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Val219Met",
"transcript": "NM_001440717.1",
"protein_id": "NP_001427646.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 522,
"cds_start": 655,
"cds_end": null,
"cds_length": 1569,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 6842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Val238Met",
"transcript": "NM_001440718.1",
"protein_id": "NP_001427647.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 517,
"cds_start": 712,
"cds_end": null,
"cds_length": 1554,
"cdna_start": 753,
"cdna_end": null,
"cdna_length": 6827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.607G>A",
"hgvs_p": "p.Val203Met",
"transcript": "NM_001440719.1",
"protein_id": "NP_001427648.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 506,
"cds_start": 607,
"cds_end": null,
"cds_length": 1521,
"cdna_start": 648,
"cdna_end": null,
"cdna_length": 6794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Val201Met",
"transcript": "NM_001440720.1",
"protein_id": "NP_001427649.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 504,
"cds_start": 601,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 948,
"cdna_end": null,
"cdna_length": 7094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.556G>A",
"hgvs_p": "p.Val186Met",
"transcript": "NM_001440721.1",
"protein_id": "NP_001427650.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 489,
"cds_start": 556,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 6743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.499G>A",
"hgvs_p": "p.Val167Met",
"transcript": "NM_001440722.1",
"protein_id": "NP_001427651.1",
"transcript_support_level": null,
"aa_start": 167,
"aa_end": null,
"aa_length": 470,
"cds_start": 499,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 540,
"cdna_end": null,
"cdna_length": 6686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"hgvs_c": "c.868G>A",
"hgvs_p": "p.Val290Met",
"transcript": "XM_047426725.1",
"protein_id": "XP_047282681.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 593,
"cds_start": 868,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1127,
"cdna_end": null,
"cdna_length": 7273,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000256789",
"gene_hgnc_id": 58146,
"hgvs_c": "n.365+5760C>T",
"hgvs_p": null,
"transcript": "ENST00000540307.2",
"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": 729,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LNCROPM",
"gene_hgnc_id": 58146,
"hgvs_c": "n.350+5760C>T",
"hgvs_p": null,
"transcript": "NR_199012.1",
"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": 714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATL3",
"gene_hgnc_id": 24526,
"dbsnp": "rs745535328",
"frequency_reference_population": 0.000034252334,
"hom_count_reference_population": 0,
"allele_count_reference_population": 55,
"gnomad_exomes_af": 0.0000343973,
"gnomad_genomes_af": 0.0000328675,
"gnomad_exomes_ac": 50,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3583102822303772,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.7540000081062317,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.407,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2107,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.638,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.996832481481497,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000398868.8",
"gene_symbol": "ATL3",
"hgnc_id": 24526,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Val238Met"
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000540307.2",
"gene_symbol": "ENSG00000256789",
"hgnc_id": 58146,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.365+5760C>T",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NR_199012.1",
"gene_symbol": "LNCROPM",
"hgnc_id": 58146,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.350+5760C>T",
"hgvs_p": null
}
],
"clinvar_disease": " hereditary sensory, type 1F,Inborn genetic diseases,Neuropathy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Neuropathy, hereditary sensory, type 1F|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}