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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: X-74525834-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=74525834&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC16A2",
"hgnc_id": 10923,
"hgvs_c": "c.1111C>T",
"hgvs_p": "p.Arg371Cys",
"inheritance_mode": "XL",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_006517.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.8938,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.3,
"chr": "X",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Allan-Herndon-Dudley syndrome,Hereditary spastic paraplegia,Inborn genetic diseases,Spastic paraplegia,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:3",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9602787494659424,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 539,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4128,
"cdna_start": 1256,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_006517.5",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1111C>T",
"hgvs_p": "p.Arg371Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000587091.6",
"protein_coding": true,
"protein_id": "NP_006508.2",
"strand": true,
"transcript": "NM_006517.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 539,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4128,
"cdna_start": 1256,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1111,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000587091.6",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1111C>T",
"hgvs_p": "p.Arg371Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006517.5",
"protein_coding": true,
"protein_id": "ENSP00000465734.1",
"strand": true,
"transcript": "ENST00000587091.6",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 577,
"aa_ref": "R",
"aa_start": 409,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4200,
"cdna_start": 1336,
"cds_end": null,
"cds_length": 1734,
"cds_start": 1225,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000878592.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1225C>T",
"hgvs_p": "p.Arg409Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548651.1",
"strand": true,
"transcript": "ENST00000878592.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 565,
"aa_ref": "R",
"aa_start": 397,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4203,
"cdna_start": 1334,
"cds_end": null,
"cds_length": 1698,
"cds_start": 1189,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000922847.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1189C>T",
"hgvs_p": "p.Arg397Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592906.1",
"strand": true,
"transcript": "ENST00000922847.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 561,
"aa_ref": "R",
"aa_start": 393,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4306,
"cdna_start": 1432,
"cds_end": null,
"cds_length": 1686,
"cds_start": 1177,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000922843.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1177C>T",
"hgvs_p": "p.Arg393Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592902.1",
"strand": true,
"transcript": "ENST00000922843.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 537,
"aa_ref": "R",
"aa_start": 369,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2846,
"cdna_start": 1228,
"cds_end": null,
"cds_length": 1614,
"cds_start": 1105,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000878593.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1105C>T",
"hgvs_p": "p.Arg369Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548652.1",
"strand": true,
"transcript": "ENST00000878593.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 480,
"aa_ref": "R",
"aa_start": 312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3950,
"cdna_start": 1079,
"cds_end": null,
"cds_length": 1443,
"cds_start": 934,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000922846.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.934C>T",
"hgvs_p": "p.Arg312Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592905.1",
"strand": true,
"transcript": "ENST00000922846.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 461,
"aa_ref": "R",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3894,
"cdna_start": 1022,
"cds_end": null,
"cds_length": 1386,
"cds_start": 877,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000878589.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.877C>T",
"hgvs_p": "p.Arg293Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548648.1",
"strand": true,
"transcript": "ENST00000878589.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 445,
"aa_ref": "R",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3901,
"cdna_start": 1027,
"cds_end": null,
"cds_length": 1338,
"cds_start": 829,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000878588.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.829C>T",
"hgvs_p": "p.Arg277Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548647.1",
"strand": true,
"transcript": "ENST00000878588.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 228,
"aa_ref": "R",
"aa_start": 184,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1886,
"cdna_start": 551,
"cds_end": null,
"cds_length": 687,
"cds_start": 550,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000590447.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.550C>T",
"hgvs_p": "p.Arg184Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466213.1",
"strand": true,
"transcript": "ENST00000590447.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 509,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4022,
"cdna_start": null,
"cds_end": null,
"cds_length": 1530,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000878591.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1080+31C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548650.1",
"strand": true,
"transcript": "ENST00000878591.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 495,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1803,
"cdna_start": null,
"cds_end": null,
"cds_length": 1488,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961799.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1027-48C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000631858.1",
"strand": true,
"transcript": "ENST00000961799.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 491,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4037,
"cdna_start": null,
"cds_end": null,
"cds_length": 1476,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000922844.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.1026+1025C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592903.1",
"strand": true,
"transcript": "ENST00000922844.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 397,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3694,
"cdna_start": null,
"cds_end": null,
"cds_length": 1194,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000878590.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.744+1025C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000548649.1",
"strand": true,
"transcript": "ENST00000878590.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 216,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3171,
"cdna_start": null,
"cds_end": null,
"cds_length": 651,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000922845.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "c.431-5499C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592904.1",
"strand": true,
"transcript": "ENST00000922845.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3893,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000636771.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "n.*812C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490445.1",
"strand": true,
"transcript": "ENST00000636771.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3893,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000636771.1",
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"hgvs_c": "n.*812C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490445.1",
"strand": true,
"transcript": "ENST00000636771.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587784384",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 10923,
"gene_symbol": "SLC16A2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Allan-Herndon-Dudley syndrome|not provided|Inborn genetic diseases|Spastic paraplegia|Hereditary spastic paraplegia",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.765,
"pos": 74525834,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.637,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_006517.5"
}
]
}