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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: 4-87980078-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=87980078&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 87980078,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001251830.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "NM_001040058.2",
"protein_id": "NP_001035147.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 314,
"cds_start": 126,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000395080.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001040058.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "ENST00000395080.8",
"protein_id": "ENSP00000378517.3",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 314,
"cds_start": 126,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001040058.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395080.8"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "ENST00000237623.11",
"protein_id": "ENSP00000237623.7",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 300,
"cds_start": 126,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000237623.11"
},
{
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.94-315A>G",
"hgvs_p": null,
"transcript": "ENST00000360804.4",
"protein_id": "ENSP00000354042.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 287,
"cds_start": null,
"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": "ENST00000360804.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.224A>G",
"hgvs_p": null,
"transcript": "ENST00000508002.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000508002.5"
},
{
"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": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.415A>G",
"hgvs_p": null,
"transcript": "ENST00000509659.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000509659.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.165A>G",
"hgvs_p": "p.Thr55Thr",
"transcript": "NM_001251830.2",
"protein_id": "NP_001238759.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 327,
"cds_start": 165,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001251830.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "ENST00000614857.5",
"protein_id": "ENSP00000477824.2",
"transcript_support_level": 2,
"aa_start": 42,
"aa_end": null,
"aa_length": 314,
"cds_start": 126,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000614857.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "ENST00000882523.1",
"protein_id": "ENSP00000552582.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 314,
"cds_start": 126,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882523.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "ENST00000942419.1",
"protein_id": "ENSP00000612478.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 314,
"cds_start": 126,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942419.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.117A>G",
"hgvs_p": "p.Thr39Thr",
"transcript": "ENST00000882522.1",
"protein_id": "ENSP00000552581.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 311,
"cds_start": 117,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882522.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "NM_000582.3",
"protein_id": "NP_000573.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 300,
"cds_start": 126,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000582.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "ENST00000942420.1",
"protein_id": "ENSP00000612479.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 300,
"cds_start": 126,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942420.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.117A>G",
"hgvs_p": "p.Thr39Thr",
"transcript": "ENST00000882525.1",
"protein_id": "ENSP00000552584.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 297,
"cds_start": 117,
"cds_end": null,
"cds_length": 894,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882525.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.126A>G",
"hgvs_p": "p.Thr42Thr",
"transcript": "ENST00000682655.1",
"protein_id": "ENSP00000508280.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 192,
"cds_start": 126,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682655.1"
},
{
"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": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.94-25A>G",
"hgvs_p": null,
"transcript": "ENST00000920430.1",
"protein_id": "ENSP00000590489.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 295,
"cds_start": null,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920430.1"
},
{
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.94-315A>G",
"hgvs_p": null,
"transcript": "NM_001040060.2",
"protein_id": "NP_001035149.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 287,
"cds_start": null,
"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": "NM_001040060.2"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.94-315A>G",
"hgvs_p": null,
"transcript": "ENST00000882524.1",
"protein_id": "ENSP00000552583.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 287,
"cds_start": null,
"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": "ENST00000882524.1"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.94-1397A>G",
"hgvs_p": null,
"transcript": "NM_001251829.2",
"protein_id": "NP_001238758.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"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": "NM_001251829.2"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.94-1397A>G",
"hgvs_p": null,
"transcript": "ENST00000508233.6",
"protein_id": "ENSP00000422973.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"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": "ENST00000508233.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.142A>G",
"hgvs_p": null,
"transcript": "ENST00000505146.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000505146.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.425A>G",
"hgvs_p": null,
"transcript": "ENST00000509334.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000509334.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
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],
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"computational_score_selected": -0.8100000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
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"bayesdelnoaf_score": -0.81,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.114,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
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"acmg_score": -17,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001251830.2",
"gene_symbol": "SPP1",
"hgnc_id": 11255,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.165A>G",
"hgvs_p": "p.Thr55Thr"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000662475.1",
"gene_symbol": "ENSG00000286618",
"hgnc_id": null,
"effects": [
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],
"inheritance_mode": "",
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}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}