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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: 6-5216622-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=5216622&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 5216622,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001164840.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "NM_020408.6",
"protein_id": "NP_065141.3",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 91,
"cds_start": 203,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000330636.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020408.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "ENST00000330636.9",
"protein_id": "ENSP00000418787.1",
"transcript_support_level": 1,
"aa_start": 68,
"aa_end": null,
"aa_length": 91,
"cds_start": 203,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020408.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000330636.9"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "ENST00000480566.5",
"protein_id": "ENSP00000419928.1",
"transcript_support_level": 1,
"aa_start": 68,
"aa_end": null,
"aa_length": 70,
"cds_start": 203,
"cds_end": null,
"cds_length": 213,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000480566.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.86+44026G>A",
"hgvs_p": null,
"transcript": "ENST00000468929.5",
"protein_id": "ENSP00000418321.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 40,
"cds_start": null,
"cds_end": null,
"cds_length": 123,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468929.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "n.116G>A",
"hgvs_p": null,
"transcript": "ENST00000463032.5",
"protein_id": "ENSP00000417885.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000463032.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "NM_001164840.3",
"protein_id": "NP_001158312.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 130,
"cds_start": 203,
"cds_end": null,
"cds_length": 393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164840.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "ENST00000500576.4",
"protein_id": "ENSP00000443900.3",
"transcript_support_level": 2,
"aa_start": 68,
"aa_end": null,
"aa_length": 130,
"cds_start": 203,
"cds_end": null,
"cds_length": 393,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000500576.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "NM_001318783.1",
"protein_id": "NP_001305712.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 115,
"cds_start": 203,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318783.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "NM_001164841.3",
"protein_id": "NP_001158313.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 96,
"cds_start": 203,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164841.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "ENST00000464010.5",
"protein_id": "ENSP00000420026.1",
"transcript_support_level": 3,
"aa_start": 68,
"aa_end": null,
"aa_length": 96,
"cds_start": 203,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000464010.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63Gln",
"transcript": "ENST00000912483.1",
"protein_id": "ENSP00000582542.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 86,
"cds_start": 188,
"cds_end": null,
"cds_length": 261,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912483.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "NM_001318782.1",
"protein_id": "NP_001305711.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 70,
"cds_start": 203,
"cds_end": null,
"cds_length": 213,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318782.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "XM_017011084.3",
"protein_id": "XP_016866573.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 129,
"cds_start": 203,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017011084.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln",
"transcript": "XM_017011083.3",
"protein_id": "XP_016866572.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 97,
"cds_start": 203,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017011083.3"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "n.420G>A",
"hgvs_p": null,
"transcript": "NR_104417.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_104417.2"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "n.420G>A",
"hgvs_p": null,
"transcript": "NR_134856.1",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_134856.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000299871",
"gene_hgnc_id": null,
"hgvs_c": "n.653+3208C>T",
"hgvs_p": null,
"transcript": "ENST00000767015.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000767015.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000299871",
"gene_hgnc_id": null,
"hgvs_c": "n.79+3208C>T",
"hgvs_p": null,
"transcript": "ENST00000767016.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000767016.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"hgvs_c": "n.303+44026G>A",
"hgvs_p": null,
"transcript": "NR_104418.1",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_104418.1"
},
{
"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": 3,
"intron_rank_end": null,
"gene_symbol": "LYRM4-AS1",
"gene_hgnc_id": 52055,
"hgvs_c": "n.374-21086C>T",
"hgvs_p": null,
"transcript": "NR_126015.1",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_126015.1"
}
],
"gene_symbol": "LYRM4",
"gene_hgnc_id": 21365,
"dbsnp": "rs587777218",
"frequency_reference_population": 0.0000027365397,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273654,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8883382081985474,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.517,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4215,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.773,
"phylop100way_prediction": "Uncertain_significance",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001164840.3",
"gene_symbol": "LYRM4",
"hgnc_id": 21365,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Gln"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NR_126015.1",
"gene_symbol": "LYRM4-AS1",
"hgnc_id": 52055,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.374-21086C>T",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000767015.1",
"gene_symbol": "ENSG00000299871",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.653+3208C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}