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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: 2-38689828-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=38689828&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 38689828,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_138801.3",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "NM_138801.3",
"protein_id": "NP_620156.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 342,
"cds_start": 568,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000272252.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138801.3"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "ENST00000272252.10",
"protein_id": "ENSP00000272252.5",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 342,
"cds_start": 568,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_138801.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000272252.10"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "ENST00000862593.1",
"protein_id": "ENSP00000532652.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 383,
"cds_start": 568,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862593.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "ENST00000862591.1",
"protein_id": "ENSP00000532650.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 382,
"cds_start": 568,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862591.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "ENST00000862589.1",
"protein_id": "ENSP00000532648.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 377,
"cds_start": 568,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862589.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.622A>T",
"hgvs_p": "p.Asn208Tyr",
"transcript": "ENST00000862592.1",
"protein_id": "ENSP00000532651.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 360,
"cds_start": 622,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862592.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "ENST00000953226.1",
"protein_id": "ENSP00000623285.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 355,
"cds_start": 568,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953226.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.592A>T",
"hgvs_p": "p.Asn198Tyr",
"transcript": "ENST00000953224.1",
"protein_id": "ENSP00000623283.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 350,
"cds_start": 592,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953224.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "ENST00000862588.1",
"protein_id": "ENSP00000532647.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 341,
"cds_start": 568,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862588.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.361A>T",
"hgvs_p": "p.Asn121Tyr",
"transcript": "ENST00000953225.1",
"protein_id": "ENSP00000623284.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 273,
"cds_start": 361,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953225.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.208A>T",
"hgvs_p": "p.Asn70Tyr",
"transcript": "ENST00000434934.1",
"protein_id": "ENSP00000399473.1",
"transcript_support_level": 3,
"aa_start": 70,
"aa_end": null,
"aa_length": 218,
"cds_start": 208,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000434934.1"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "XM_011532540.3",
"protein_id": "XP_011530842.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 221,
"cds_start": 568,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532540.3"
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr",
"transcript": "XM_047443419.1",
"protein_id": "XP_047299375.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 221,
"cds_start": 568,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443419.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.552+8342A>T",
"hgvs_p": null,
"transcript": "ENST00000862590.1",
"protein_id": "ENSP00000532649.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 291,
"cds_start": null,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862590.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.190+23477A>T",
"hgvs_p": null,
"transcript": "ENST00000410063.5",
"protein_id": "ENSP00000386233.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 194,
"cds_start": null,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000410063.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "n.487A>T",
"hgvs_p": null,
"transcript": "ENST00000444351.5",
"protein_id": "ENSP00000409083.1",
"transcript_support_level": 5,
"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": "ENST00000444351.5"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124905993",
"gene_hgnc_id": null,
"hgvs_c": "n.220-4154T>A",
"hgvs_p": null,
"transcript": "XR_007086292.1",
"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": "XR_007086292.1"
}
],
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"dbsnp": "rs6741892",
"frequency_reference_population": 0.09813157,
"hom_count_reference_population": 9958,
"allele_count_reference_population": 157205,
"gnomad_exomes_af": 0.09441,
"gnomad_genomes_af": 0.133585,
"gnomad_exomes_ac": 136875,
"gnomad_genomes_ac": 20330,
"gnomad_exomes_homalt": 8198,
"gnomad_genomes_homalt": 1760,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0011598765850067139,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.107,
"revel_prediction": "Benign",
"alphamissense_score": 0.0523,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.23,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_138801.3",
"gene_symbol": "GALM",
"hgnc_id": 24063,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.568A>T",
"hgvs_p": "p.Asn190Tyr"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_007086292.1",
"gene_symbol": "LOC124905993",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.220-4154T>A",
"hgvs_p": null
}
],
"clinvar_disease": "GALM-related disorder,Galactosemia 4,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not provided|Galactosemia 4|GALM-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}