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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: 3-48688580-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=48688580&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 48688580,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016291.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "NM_016291.4",
"protein_id": "NP_057375.2",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000328631.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016291.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000328631.10",
"protein_id": "ENSP00000331103.5",
"transcript_support_level": 1,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016291.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000328631.10"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"transcript": "ENST00000921848.1",
"protein_id": "ENSP00000591907.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 449,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921848.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"transcript": "ENST00000921850.1",
"protein_id": "ENSP00000591909.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 449,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921850.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"transcript": "ENST00000921857.1",
"protein_id": "ENSP00000591916.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 449,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921857.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"transcript": "ENST00000946886.1",
"protein_id": "ENSP00000616945.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 449,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946886.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.1037G>A",
"hgvs_p": "p.Arg346His",
"transcript": "ENST00000904745.1",
"protein_id": "ENSP00000574804.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 447,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904745.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339His",
"transcript": "ENST00000946882.1",
"protein_id": "ENSP00000616941.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 440,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946882.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "NM_001005909.3",
"protein_id": "NP_001005909.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001005909.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000904743.1",
"protein_id": "ENSP00000574802.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904743.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000904744.1",
"protein_id": "ENSP00000574803.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904744.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000904746.1",
"protein_id": "ENSP00000574805.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904746.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000904748.1",
"protein_id": "ENSP00000574807.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904748.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921847.1",
"protein_id": "ENSP00000591906.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921847.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921849.1",
"protein_id": "ENSP00000591908.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921849.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921851.1",
"protein_id": "ENSP00000591910.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921851.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921852.1",
"protein_id": "ENSP00000591911.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921852.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921853.1",
"protein_id": "ENSP00000591912.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921853.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921854.1",
"protein_id": "ENSP00000591913.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921854.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921855.1",
"protein_id": "ENSP00000591914.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921855.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000921856.1",
"protein_id": "ENSP00000591915.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921856.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "IP6K2",
"gene_hgnc_id": 17313,
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His",
"transcript": "ENST00000946876.1",
"protein_id": "ENSP00000616935.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 426,
"cds_start": 974,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
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"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533818.2"
}
],
"gene_symbol": "IP6K2",
"gene_hgnc_id": 17313,
"dbsnp": "rs1020131272",
"frequency_reference_population": 0.0000018586186,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.0000013681,
"gnomad_genomes_af": 0.00000656961,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9631969928741455,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.678,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9836,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.905,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_016291.4",
"gene_symbol": "IP6K2",
"hgnc_id": 17313,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.974G>A",
"hgvs_p": "p.Arg325His"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}