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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: 2-38666166-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=38666166&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 38666166,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_138801.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "NM_138801.3",
"protein_id": "NP_620156.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 342,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000272252.10",
"protein_id": "ENSP00000272252.5",
"transcript_support_level": 1,
"aa_start": 2,
"aa_end": null,
"aa_length": 342,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000862593.1",
"protein_id": "ENSP00000532652.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 383,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000862591.1",
"protein_id": "ENSP00000532650.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 382,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000862589.1",
"protein_id": "ENSP00000532648.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 377,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000862592.1",
"protein_id": "ENSP00000532651.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 360,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000953226.1",
"protein_id": "ENSP00000623285.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 355,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000953224.1",
"protein_id": "ENSP00000623283.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 350,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000862588.1",
"protein_id": "ENSP00000532647.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 341,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000862590.1",
"protein_id": "ENSP00000532649.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 291,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000953225.1",
"protein_id": "ENSP00000623284.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 273,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000410063.5",
"protein_id": "ENSP00000386233.1",
"transcript_support_level": 3,
"aa_start": 2,
"aa_end": null,
"aa_length": 194,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "XM_011532540.3",
"protein_id": "XP_011530842.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 221,
"cds_start": 5,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "XM_047443419.1",
"protein_id": "XP_047299375.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 221,
"cds_start": 5,
"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": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "n.86C>T",
"hgvs_p": null,
"transcript": "ENST00000427858.4",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000427858.4"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GALM-AS1",
"gene_hgnc_id": 41037,
"hgvs_c": "n.478+2511G>A",
"hgvs_p": null,
"transcript": "ENST00000756141.1",
"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": "ENST00000756141.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"hgvs_c": "n.-77C>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"
}
],
"gene_symbol": "GALM",
"gene_hgnc_id": 24063,
"dbsnp": "rs1159501195",
"frequency_reference_population": 0.0000013713395,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137134,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07270610332489014,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.024,
"revel_prediction": "Benign",
"alphamissense_score": 0.1345,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.508,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_138801.3",
"gene_symbol": "GALM",
"hgnc_id": 24063,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000756141.1",
"gene_symbol": "GALM-AS1",
"hgnc_id": 41037,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.478+2511G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}