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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: 16-5084766-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=5084766&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 5084766,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_019109.5",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1280T>G",
"hgvs_p": "p.Phe427Cys",
"transcript": "NM_019109.5",
"protein_id": "NP_061982.3",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 464,
"cds_start": 1280,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1287,
"cdna_end": null,
"cdna_length": 3900,
"mane_select": "ENST00000262374.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019109.5"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1280T>G",
"hgvs_p": "p.Phe427Cys",
"transcript": "ENST00000262374.10",
"protein_id": "ENSP00000262374.5",
"transcript_support_level": 1,
"aa_start": 427,
"aa_end": null,
"aa_length": 464,
"cds_start": 1280,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1287,
"cdna_end": null,
"cdna_length": 3900,
"mane_select": "NM_019109.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262374.10"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.947T>G",
"hgvs_p": "p.Phe316Cys",
"transcript": "ENST00000588623.5",
"protein_id": "ENSP00000468118.1",
"transcript_support_level": 1,
"aa_start": 316,
"aa_end": null,
"aa_length": 353,
"cds_start": 947,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 2047,
"cdna_end": null,
"cdna_length": 2671,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000588623.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EEF2KMT",
"gene_hgnc_id": 32221,
"hgvs_c": "c.*866A>C",
"hgvs_p": null,
"transcript": "NM_201400.4",
"protein_id": "NP_958802.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 330,
"cds_start": null,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2397,
"mane_select": "ENST00000427587.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_201400.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EEF2KMT",
"gene_hgnc_id": 32221,
"hgvs_c": "c.*866A>C",
"hgvs_p": null,
"transcript": "ENST00000427587.9",
"protein_id": "ENSP00000398502.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 330,
"cds_start": null,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2397,
"mane_select": "NM_201400.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427587.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EEF2KMT",
"gene_hgnc_id": 32221,
"hgvs_c": "c.*866A>C",
"hgvs_p": null,
"transcript": "ENST00000458008.8",
"protein_id": "ENSP00000389710.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 296,
"cds_start": null,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2268,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000458008.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "n.*1181T>G",
"hgvs_p": null,
"transcript": "ENST00000591822.5",
"protein_id": "ENSP00000467865.1",
"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": 1689,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000591822.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "n.*1181T>G",
"hgvs_p": null,
"transcript": "ENST00000591822.5",
"protein_id": "ENSP00000467865.1",
"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": 1689,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000591822.5"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1313T>G",
"hgvs_p": "p.Phe438Cys",
"transcript": "ENST00000940711.1",
"protein_id": "ENSP00000610770.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 475,
"cds_start": 1313,
"cds_end": null,
"cds_length": 1428,
"cdna_start": 1339,
"cdna_end": null,
"cdna_length": 2148,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940711.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1304T>G",
"hgvs_p": "p.Phe435Cys",
"transcript": "ENST00000902497.1",
"protein_id": "ENSP00000572556.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 472,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1311,
"cdna_end": null,
"cdna_length": 2150,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902497.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1271T>G",
"hgvs_p": "p.Phe424Cys",
"transcript": "ENST00000940712.1",
"protein_id": "ENSP00000610771.1",
"transcript_support_level": null,
"aa_start": 424,
"aa_end": null,
"aa_length": 461,
"cds_start": 1271,
"cds_end": null,
"cds_length": 1386,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 1913,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940712.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1244T>G",
"hgvs_p": "p.Phe415Cys",
"transcript": "ENST00000961949.1",
"protein_id": "ENSP00000632008.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 452,
"cds_start": 1244,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 1269,
"cdna_end": null,
"cdna_length": 1888,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961949.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1241T>G",
"hgvs_p": "p.Phe414Cys",
"transcript": "NM_001438123.1",
"protein_id": "NP_001425052.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 451,
"cds_start": 1241,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1248,
"cdna_end": null,
"cdna_length": 3861,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438123.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1241T>G",
"hgvs_p": "p.Phe414Cys",
"transcript": "ENST00000684190.1",
"protein_id": "ENSP00000507554.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 451,
"cds_start": 1241,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1285,
"cdna_end": null,
"cdna_length": 2051,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000684190.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1220T>G",
"hgvs_p": "p.Phe407Cys",
"transcript": "ENST00000902499.1",
"protein_id": "ENSP00000572558.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 444,
"cds_start": 1220,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 1221,
"cdna_end": null,
"cdna_length": 1498,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902499.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1169T>G",
"hgvs_p": "p.Phe390Cys",
"transcript": "ENST00000684335.1",
"protein_id": "ENSP00000508112.1",
"transcript_support_level": null,
"aa_start": 390,
"aa_end": null,
"aa_length": 427,
"cds_start": 1169,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 1213,
"cdna_end": null,
"cdna_length": 1952,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000684335.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1169T>G",
"hgvs_p": "p.Phe390Cys",
"transcript": "ENST00000902498.1",
"protein_id": "ENSP00000572557.1",
"transcript_support_level": null,
"aa_start": 390,
"aa_end": null,
"aa_length": 427,
"cds_start": 1169,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 1176,
"cdna_end": null,
"cdna_length": 1994,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902498.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1130T>G",
"hgvs_p": "p.Phe377Cys",
"transcript": "ENST00000961948.1",
"protein_id": "ENSP00000632007.1",
"transcript_support_level": null,
"aa_start": 377,
"aa_end": null,
"aa_length": 414,
"cds_start": 1130,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 1777,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961948.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.1109T>G",
"hgvs_p": "p.Phe370Cys",
"transcript": "ENST00000940713.1",
"protein_id": "ENSP00000610772.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 407,
"cds_start": 1109,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 1110,
"cdna_end": null,
"cdna_length": 1727,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940713.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.947T>G",
"hgvs_p": "p.Phe316Cys",
"transcript": "NM_001330504.2",
"protein_id": "NP_001317433.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 353,
"cds_start": 947,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 1128,
"cdna_end": null,
"cdna_length": 3741,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330504.2"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.947T>G",
"hgvs_p": "p.Phe316Cys",
"transcript": "ENST00000544428.1",
"protein_id": "ENSP00000440019.1",
"transcript_support_level": 2,
"aa_start": 316,
"aa_end": null,
"aa_length": 353,
"cds_start": 947,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 1128,
"cdna_end": null,
"cdna_length": 1419,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544428.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG1",
"gene_hgnc_id": 18294,
"hgvs_c": "c.947T>G",
"hgvs_p": "p.Phe316Cys",
"transcript": "ENST00000683739.1",
"protein_id": "ENSP00000507002.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 353,
"cds_start": 947,
"cds_end": null,
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],
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"dbsnp": "rs1957090242",
"frequency_reference_population": 6.924565e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.92457e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8362919092178345,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.717,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6385,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.686,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
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"acmg_by_gene": [
{
"score": 4,
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"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_019109.5",
"gene_symbol": "ALG1",
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"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
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"hgvs_p": "p.Phe427Cys"
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{
"score": 4,
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"criteria": [
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"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
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],
"inheritance_mode": "AR",
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}
],
"clinvar_disease": "ALG1-congenital disorder of glycosylation",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "ALG1-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}