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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: 22-50625446-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=50625446&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 50625446,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000216124.10",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "NM_000487.6",
"protein_id": "NP_000478.3",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1602,
"cdna_end": null,
"cdna_length": 4294,
"mane_select": "ENST00000216124.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "ENST00000216124.10",
"protein_id": "ENSP00000216124.5",
"transcript_support_level": 1,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1602,
"cdna_end": null,
"cdna_length": 4294,
"mane_select": "NM_000487.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "ENST00000356098.9",
"protein_id": "ENSP00000348406.5",
"transcript_support_level": 1,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1467,
"cdna_end": null,
"cdna_length": 1895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "NM_001085425.3",
"protein_id": "NP_001078894.2",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1497,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "NM_001085426.3",
"protein_id": "NP_001078895.2",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1449,
"cdna_end": null,
"cdna_length": 4141,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "NM_001085427.3",
"protein_id": "NP_001078896.2",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1404,
"cdna_end": null,
"cdna_length": 4096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "ENST00000395619.3",
"protein_id": "ENSP00000378981.3",
"transcript_support_level": 5,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1411,
"cdna_end": null,
"cdna_length": 1824,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile",
"transcript": "ENST00000395621.7",
"protein_id": "ENSP00000378983.3",
"transcript_support_level": 2,
"aa_start": 410,
"aa_end": null,
"aa_length": 509,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1500,
"cdna_end": null,
"cdna_length": 1918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.971C>T",
"hgvs_p": "p.Thr324Ile",
"transcript": "NM_001085428.3",
"protein_id": "NP_001078897.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 423,
"cds_start": 971,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 1212,
"cdna_end": null,
"cdna_length": 3904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.971C>T",
"hgvs_p": "p.Thr324Ile",
"transcript": "NM_001362782.2",
"protein_id": "NP_001349711.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 423,
"cds_start": 971,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 1167,
"cdna_end": null,
"cdna_length": 3859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.971C>T",
"hgvs_p": "p.Thr324Ile",
"transcript": "ENST00000453344.6",
"protein_id": "ENSP00000412542.2",
"transcript_support_level": 2,
"aa_start": 324,
"aa_end": null,
"aa_length": 423,
"cds_start": 971,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 1650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1126C>T",
"hgvs_p": "p.Pro376Ser",
"transcript": "XM_011530691.4",
"protein_id": "XP_011528993.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 387,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1499,
"cdna_end": null,
"cdna_length": 4191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1126C>T",
"hgvs_p": "p.Pro376Ser",
"transcript": "XM_024452241.2",
"protein_id": "XP_024308009.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 387,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 4038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "c.1126C>T",
"hgvs_p": "p.Pro376Ser",
"transcript": "XM_047441363.1",
"protein_id": "XP_047297319.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 387,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1301,
"cdna_end": null,
"cdna_length": 3993,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"hgvs_c": "n.95C>T",
"hgvs_p": null,
"transcript": "ENST00000608497.1",
"protein_id": "ENSP00000477013.1",
"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": 576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARSA",
"gene_hgnc_id": 713,
"dbsnp": "rs28940895",
"frequency_reference_population": 0.0000056223225,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000552258,
"gnomad_genomes_af": 0.00000657186,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7338428497314453,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.2800000011920929,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.561,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.293,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.28,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000216124.10",
"gene_symbol": "ARSA",
"hgnc_id": 713,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1229C>T",
"hgvs_p": "p.Thr410Ile"
}
],
"clinvar_disease": " adult type,Metachromatic leukodystrophy",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Metachromatic leukodystrophy, adult type|Metachromatic leukodystrophy",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}