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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: X-79361124-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=79361124&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 79361124,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004867.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.757G>A",
"hgvs_p": "p.Glu253Lys",
"transcript": "NM_004867.5",
"protein_id": "NP_004858.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 263,
"cds_start": 757,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000373298.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004867.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.757G>A",
"hgvs_p": "p.Glu253Lys",
"transcript": "ENST00000373298.7",
"protein_id": "ENSP00000362395.2",
"transcript_support_level": 1,
"aa_start": 253,
"aa_end": null,
"aa_length": 263,
"cds_start": 757,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004867.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373298.7"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.757G>A",
"hgvs_p": "p.Glu253Lys",
"transcript": "ENST00000865381.1",
"protein_id": "ENSP00000535440.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 263,
"cds_start": 757,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865381.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.757G>A",
"hgvs_p": "p.Glu253Lys",
"transcript": "ENST00000865383.1",
"protein_id": "ENSP00000535442.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 263,
"cds_start": 757,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865383.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.754G>A",
"hgvs_p": "p.Glu252Lys",
"transcript": "ENST00000933703.1",
"protein_id": "ENSP00000603762.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 262,
"cds_start": 754,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933703.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Glu244Lys",
"transcript": "ENST00000933705.1",
"protein_id": "ENSP00000603764.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 254,
"cds_start": 730,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933705.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Glu244Lys",
"transcript": "ENST00000944509.1",
"protein_id": "ENSP00000614568.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 254,
"cds_start": 730,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944509.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.715G>A",
"hgvs_p": "p.Glu239Lys",
"transcript": "ENST00000944508.1",
"protein_id": "ENSP00000614567.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 249,
"cds_start": 715,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944508.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.646G>A",
"hgvs_p": "p.Glu216Lys",
"transcript": "ENST00000933706.1",
"protein_id": "ENSP00000603765.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 226,
"cds_start": 646,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933706.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Glu209Lys",
"transcript": "NM_001171581.2",
"protein_id": "NP_001165052.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 219,
"cds_start": 625,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171581.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Glu209Lys",
"transcript": "ENST00000434584.2",
"protein_id": "ENSP00000415533.2",
"transcript_support_level": 2,
"aa_start": 209,
"aa_end": null,
"aa_length": 219,
"cds_start": 625,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000434584.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Glu209Lys",
"transcript": "ENST00000865382.1",
"protein_id": "ENSP00000535441.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 219,
"cds_start": 625,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865382.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Glu209Lys",
"transcript": "ENST00000933702.1",
"protein_id": "ENSP00000603761.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 219,
"cds_start": 625,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933702.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "c.598G>A",
"hgvs_p": "p.Glu200Lys",
"transcript": "ENST00000933704.1",
"protein_id": "ENSP00000603763.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 210,
"cds_start": 598,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933704.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITM2A",
"gene_hgnc_id": 6173,
"hgvs_c": "n.717G>A",
"hgvs_p": null,
"transcript": "ENST00000469541.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000469541.5"
}
],
"gene_symbol": "ITM2A",
"gene_hgnc_id": 6173,
"dbsnp": null,
"frequency_reference_population": 0.00000734538,
"hom_count_reference_population": 3,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000734538,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10234853625297546,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.069,
"revel_prediction": "Benign",
"alphamissense_score": 0.1594,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.288,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_004867.5",
"gene_symbol": "ITM2A",
"hgnc_id": 6173,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.757G>A",
"hgvs_p": "p.Glu253Lys"
}
],
"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
}