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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: 16-8847724-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=8847724&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 8847724,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000303.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "c.640G>A",
"hgvs_p": "p.Gly214Ser",
"transcript": "NM_000303.3",
"protein_id": "NP_000294.1",
"transcript_support_level": null,
"aa_start": 214,
"aa_end": null,
"aa_length": 246,
"cds_start": 640,
"cds_end": null,
"cds_length": 741,
"cdna_start": 684,
"cdna_end": null,
"cdna_length": 2285,
"mane_select": "ENST00000268261.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "c.640G>A",
"hgvs_p": "p.Gly214Ser",
"transcript": "ENST00000268261.9",
"protein_id": "ENSP00000268261.4",
"transcript_support_level": 1,
"aa_start": 214,
"aa_end": null,
"aa_length": 246,
"cds_start": 640,
"cds_end": null,
"cds_length": 741,
"cdna_start": 684,
"cdna_end": null,
"cdna_length": 2285,
"mane_select": "NM_000303.3",
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*258G>A",
"hgvs_p": null,
"transcript": "ENST00000565221.5",
"protein_id": "ENSP00000457932.1",
"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": 793,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*262G>A",
"hgvs_p": null,
"transcript": "ENST00000566540.5",
"protein_id": "ENSP00000454284.1",
"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": 1557,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.3808G>A",
"hgvs_p": null,
"transcript": "ENST00000567697.2",
"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": 5397,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*258G>A",
"hgvs_p": null,
"transcript": "ENST00000565221.5",
"protein_id": "ENSP00000457932.1",
"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": 793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*262G>A",
"hgvs_p": null,
"transcript": "ENST00000566540.5",
"protein_id": "ENSP00000454284.1",
"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": 1557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "c.559G>A",
"hgvs_p": "p.Gly187Ser",
"transcript": "ENST00000566983.5",
"protein_id": "ENSP00000457956.1",
"transcript_support_level": 5,
"aa_start": 187,
"aa_end": null,
"aa_length": 219,
"cds_start": 559,
"cds_end": null,
"cds_length": 660,
"cdna_start": 763,
"cdna_end": null,
"cdna_length": 907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Gly123Ser",
"transcript": "ENST00000569958.5",
"protein_id": "ENSP00000456302.1",
"transcript_support_level": 2,
"aa_start": 123,
"aa_end": null,
"aa_length": 155,
"cds_start": 367,
"cds_end": null,
"cds_length": 468,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "c.391G>A",
"hgvs_p": "p.Gly131Ser",
"transcript": "XM_047434215.1",
"protein_id": "XP_047290171.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 163,
"cds_start": 391,
"cds_end": null,
"cds_length": 492,
"cdna_start": 494,
"cdna_end": null,
"cdna_length": 2095,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.174G>A",
"hgvs_p": null,
"transcript": "ENST00000562025.1",
"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": 569,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*362G>A",
"hgvs_p": null,
"transcript": "ENST00000562318.5",
"protein_id": "ENSP00000454395.1",
"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": 931,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*180G>A",
"hgvs_p": null,
"transcript": "ENST00000566604.5",
"protein_id": "ENSP00000456774.1",
"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": 986,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260350",
"gene_hgnc_id": null,
"hgvs_c": "n.356C>T",
"hgvs_p": null,
"transcript": "ENST00000567942.1",
"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": 430,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*98G>A",
"hgvs_p": null,
"transcript": "ENST00000570076.5",
"protein_id": "ENSP00000456961.1",
"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": 1002,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*536G>A",
"hgvs_p": null,
"transcript": "ENST00000683435.1",
"protein_id": "ENSP00000508092.1",
"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": 1048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*362G>A",
"hgvs_p": null,
"transcript": "ENST00000562318.5",
"protein_id": "ENSP00000454395.1",
"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": 931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*180G>A",
"hgvs_p": null,
"transcript": "ENST00000566604.5",
"protein_id": "ENSP00000456774.1",
"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": 986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*98G>A",
"hgvs_p": null,
"transcript": "ENST00000570076.5",
"protein_id": "ENSP00000456961.1",
"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": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*536G>A",
"hgvs_p": null,
"transcript": "ENST00000683435.1",
"protein_id": "ENSP00000508092.1",
"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": 1048,
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*258-1645G>A",
"hgvs_p": null,
"transcript": "ENST00000682393.1",
"protein_id": "ENSP00000506774.1",
"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": 2606,
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*262-1645G>A",
"hgvs_p": null,
"transcript": "ENST00000683094.1",
"protein_id": "ENSP00000508230.1",
"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": 1153,
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"hgvs_c": "n.*180-1645G>A",
"hgvs_p": null,
"transcript": "ENST00000683274.1",
"protein_id": "ENSP00000507262.1",
"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": 1295,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PMM2",
"gene_hgnc_id": 9115,
"dbsnp": "rs1555453238",
"frequency_reference_population": 0.0000027423669,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000274237,
"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": 0.9915688037872314,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9179999828338623,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.976,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6283,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.295,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.22,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.998697431558488,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000303.3",
"gene_symbol": "PMM2",
"hgnc_id": 9115,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.640G>A",
"hgvs_p": "p.Gly214Ser"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000567942.1",
"gene_symbol": "ENSG00000260350",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.356C>T",
"hgvs_p": null
}
],
"clinvar_disease": "PMM2-congenital disorder of glycosylation,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:2",
"phenotype_combined": "PMM2-congenital disorder of glycosylation|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}