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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: 17-75762751-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=75762751&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GALK1",
"hgnc_id": 4118,
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_000154.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 926,
"alphamissense_prediction": null,
"alphamissense_score": 0.0801,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "17",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Deficiency of galactokinase,GALK1-related disorder",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.014584869146347046,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 392,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1397,
"cdna_start": 802,
"cds_end": null,
"cds_length": 1179,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_000154.2",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000588479.6",
"protein_coding": true,
"protein_id": "NP_000145.1",
"strand": false,
"transcript": "NM_000154.2",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 392,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1397,
"cdna_start": 802,
"cds_end": null,
"cds_length": 1179,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000588479.6",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000154.2",
"protein_coding": true,
"protein_id": "ENSP00000465930.1",
"strand": false,
"transcript": "ENST00000588479.6",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 424,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1443,
"cdna_start": 797,
"cds_end": null,
"cds_length": 1275,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000864472.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534531.1",
"strand": false,
"transcript": "ENST00000864472.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 423,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1483,
"cdna_start": 847,
"cds_end": null,
"cds_length": 1272,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000864469.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534528.1",
"strand": false,
"transcript": "ENST00000864469.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 409,
"aa_ref": "A",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1580,
"cdna_start": 857,
"cds_end": null,
"cds_length": 1230,
"cds_start": 797,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000864468.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.797C>T",
"hgvs_p": "p.Ala266Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534527.1",
"strand": false,
"transcript": "ENST00000864468.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 409,
"aa_ref": "A",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1421,
"cdna_start": 871,
"cds_end": null,
"cds_length": 1230,
"cds_start": 797,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000864470.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.797C>T",
"hgvs_p": "p.Ala266Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534529.1",
"strand": false,
"transcript": "ENST00000864470.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 392,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1526,
"cdna_start": 802,
"cds_end": null,
"cds_length": 1179,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001381985.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001368914.1",
"strand": false,
"transcript": "NM_001381985.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 392,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1445,
"cdna_start": 846,
"cds_end": null,
"cds_length": 1179,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000225614.6",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000225614.1",
"strand": false,
"transcript": "ENST00000225614.6",
"transcript_support_level": 2
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 391,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1360,
"cdna_start": 814,
"cds_end": null,
"cds_length": 1176,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000956675.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626734.1",
"strand": false,
"transcript": "ENST00000956675.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 387,
"aa_ref": "A",
"aa_start": 244,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1334,
"cdna_start": 791,
"cds_end": null,
"cds_length": 1164,
"cds_start": 731,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000864471.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.731C>T",
"hgvs_p": "p.Ala244Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534530.1",
"strand": false,
"transcript": "ENST00000864471.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 383,
"aa_ref": "A",
"aa_start": 240,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1279,
"cdna_start": 732,
"cds_end": null,
"cds_length": 1152,
"cds_start": 719,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000864474.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.719C>T",
"hgvs_p": "p.Ala240Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534533.1",
"strand": false,
"transcript": "ENST00000864474.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 362,
"aa_ref": "A",
"aa_start": 219,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1251,
"cdna_start": 656,
"cds_end": null,
"cds_length": 1089,
"cds_start": 656,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000592997.6",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.656C>T",
"hgvs_p": "p.Ala219Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000464765.2",
"strand": false,
"transcript": "ENST00000592997.6",
"transcript_support_level": 2
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 355,
"aa_ref": "A",
"aa_start": 212,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1221,
"cdna_start": 672,
"cds_end": null,
"cds_length": 1068,
"cds_start": 635,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000864473.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.635C>T",
"hgvs_p": "p.Ala212Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534532.1",
"strand": false,
"transcript": "ENST00000864473.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 352,
"aa_ref": "A",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1216,
"cdna_start": 671,
"cds_end": null,
"cds_length": 1059,
"cds_start": 626,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000937574.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.626C>T",
"hgvs_p": "p.Ala209Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607633.1",
"strand": false,
"transcript": "ENST00000937574.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 342,
"aa_ref": "A",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1261,
"cdna_start": 861,
"cds_end": null,
"cds_length": 1029,
"cds_start": 746,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000956674.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.746C>T",
"hgvs_p": "p.Ala249Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626733.1",
"strand": false,
"transcript": "ENST00000956674.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 286,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1020,
"cdna_start": null,
"cds_end": null,
"cds_length": 861,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000937573.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "c.475+569C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607632.1",
"strand": false,
"transcript": "ENST00000937573.1",
"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": 913,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000587707.2",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "n.*256C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468341.2",
"strand": false,
"transcript": "ENST00000587707.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1121,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000592494.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "n.1065C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000592494.1",
"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": 913,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000587707.2",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "n.*256C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468341.2",
"strand": false,
"transcript": "ENST00000587707.2",
"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": 1180,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000586244.1",
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"hgvs_c": "n.*768C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468288.1",
"strand": true,
"transcript": "ENST00000586244.1",
"transcript_support_level": 1
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs149825190",
"effect": "missense_variant",
"frequency_reference_population": 0.0005738294,
"gene_hgnc_id": 4118,
"gene_symbol": "GALK1",
"gnomad_exomes_ac": 828,
"gnomad_exomes_af": 0.000566517,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 98,
"gnomad_genomes_af": 0.000644067,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Deficiency of galactokinase|GALK1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.683,
"pos": 75762751,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.212,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000154.2"
}
]
}