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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: 3-39391956-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=39391956&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 39391956,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_017875.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.560G>A",
"hgvs_p": "p.Arg187Gln",
"transcript": "NM_017875.4",
"protein_id": "NP_060345.2",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 304,
"cds_start": 560,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000650617.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017875.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.560G>A",
"hgvs_p": "p.Arg187Gln",
"transcript": "ENST00000650617.1",
"protein_id": "ENSP00000497532.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 304,
"cds_start": 560,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017875.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000650617.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.560G>A",
"hgvs_p": "p.Arg187Gln",
"transcript": "ENST00000885743.1",
"protein_id": "ENSP00000555802.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 336,
"cds_start": 560,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885743.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.560G>A",
"hgvs_p": "p.Arg187Gln",
"transcript": "ENST00000949226.1",
"protein_id": "ENSP00000619285.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 335,
"cds_start": 560,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949226.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Arg185Gln",
"transcript": "ENST00000885742.1",
"protein_id": "ENSP00000555801.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 302,
"cds_start": 554,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885742.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170Gln",
"transcript": "ENST00000643672.1",
"protein_id": "ENSP00000494532.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 287,
"cds_start": 509,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000643672.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"transcript": "ENST00000645280.1",
"protein_id": "ENSP00000496690.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 286,
"cds_start": 506,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000645280.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.512G>A",
"hgvs_p": "p.Arg171Gln",
"transcript": "ENST00000642683.1",
"protein_id": "ENSP00000495376.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 247,
"cds_start": 512,
"cds_end": null,
"cds_length": 744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000642683.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.560G>A",
"hgvs_p": "p.Arg187Gln",
"transcript": "NM_001354798.2",
"protein_id": "NP_001341727.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 237,
"cds_start": 560,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354798.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.353G>A",
"hgvs_p": "p.Arg118Gln",
"transcript": "ENST00000949227.1",
"protein_id": "ENSP00000619286.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 235,
"cds_start": 353,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949227.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.332G>A",
"hgvs_p": "p.Arg111Gln",
"transcript": "ENST00000885741.1",
"protein_id": "ENSP00000555800.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 228,
"cds_start": 332,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885741.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Arg58Gln",
"transcript": "ENST00000885744.1",
"protein_id": "ENSP00000555803.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 175,
"cds_start": 173,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885744.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.380G>A",
"hgvs_p": "p.Arg127Gln",
"transcript": "ENST00000645630.1",
"protein_id": "ENSP00000493714.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 150,
"cds_start": 380,
"cds_end": null,
"cds_length": 454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000645630.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.542G>A",
"hgvs_p": "p.Arg181Gln",
"transcript": "XM_011533869.3",
"protein_id": "XP_011532171.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 298,
"cds_start": 542,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533869.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"transcript": "XM_024453611.2",
"protein_id": "XP_024309379.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 286,
"cds_start": 506,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453611.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"transcript": "XM_047448413.1",
"protein_id": "XP_047304369.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 286,
"cds_start": 506,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448413.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"transcript": "XM_047448414.1",
"protein_id": "XP_047304370.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 286,
"cds_start": 506,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448414.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"transcript": "XM_047448415.1",
"protein_id": "XP_047304371.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 286,
"cds_start": 506,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448415.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"transcript": "XM_047448416.1",
"protein_id": "XP_047304372.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 286,
"cds_start": 506,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448416.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "c.70-4442G>A",
"hgvs_p": null,
"transcript": "ENST00000929325.1",
"protein_id": "ENSP00000599384.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 63,
"cds_start": null,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929325.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"hgvs_c": "n.560G>A",
"hgvs_p": null,
"transcript": "ENST00000648579.1",
"protein_id": "ENSP00000497638.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000648579.1"
}
],
"gene_symbol": "SLC25A38",
"gene_hgnc_id": 26054,
"dbsnp": "rs121918331",
"frequency_reference_population": 0.0000049563655,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000478835,
"gnomad_genomes_af": 0.00000657013,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9833515286445618,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.807,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9424,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.516,
"phylop100way_prediction": "Pathogenic",
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_017875.4",
"gene_symbol": "SLC25A38",
"hgnc_id": 26054,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.560G>A",
"hgvs_p": "p.Arg187Gln"
}
],
"clinvar_disease": "Sideroblastic anemia 2,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:1",
"phenotype_combined": "Sideroblastic anemia 2|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}