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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: 10-98425637-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=98425637&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 98425637,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_000195.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "NM_000195.5",
"protein_id": "NP_000186.2",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361490.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000195.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000361490.9",
"protein_id": "ENSP00000355310.4",
"transcript_support_level": 1,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000195.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361490.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "n.*598G>T",
"hgvs_p": null,
"transcript": "ENST00000467246.5",
"protein_id": "ENSP00000514163.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000467246.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289758",
"gene_hgnc_id": null,
"hgvs_c": "n.*598G>T",
"hgvs_p": null,
"transcript": "ENST00000699159.1",
"protein_id": "ENSP00000514167.1",
"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": "ENST00000699159.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "n.*598G>T",
"hgvs_p": null,
"transcript": "ENST00000467246.5",
"protein_id": "ENSP00000514163.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000467246.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289758",
"gene_hgnc_id": null,
"hgvs_c": "n.*598G>T",
"hgvs_p": null,
"transcript": "ENST00000699159.1",
"protein_id": "ENSP00000514167.1",
"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": "ENST00000699159.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1497G>T",
"hgvs_p": "p.Pro499Pro",
"transcript": "ENST00000699134.1",
"protein_id": "ENSP00000514151.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 786,
"cds_start": 1497,
"cds_end": null,
"cds_length": 2361,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000699134.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1281G>T",
"hgvs_p": "p.Pro427Pro",
"transcript": "ENST00000963962.1",
"protein_id": "ENSP00000634021.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 714,
"cds_start": 1281,
"cds_end": null,
"cds_length": 2145,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963962.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1269G>T",
"hgvs_p": "p.Pro423Pro",
"transcript": "ENST00000699125.1",
"protein_id": "ENSP00000514146.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 710,
"cds_start": 1269,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000699125.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1269G>T",
"hgvs_p": "p.Pro423Pro",
"transcript": "ENST00000884309.1",
"protein_id": "ENSP00000554368.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 710,
"cds_start": 1269,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884309.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "NM_001322476.2",
"protein_id": "NP_001309405.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001322476.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "NM_001322477.2",
"protein_id": "NP_001309406.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001322477.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000325103.10",
"protein_id": "ENSP00000326649.6",
"transcript_support_level": 5,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000325103.10"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000699142.1",
"protein_id": "ENSP00000514159.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000699142.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000884307.1",
"protein_id": "ENSP00000554366.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884307.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000884313.1",
"protein_id": "ENSP00000554372.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884313.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000884316.1",
"protein_id": "ENSP00000554375.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884316.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000884317.1",
"protein_id": "ENSP00000554376.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884317.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1239G>T",
"hgvs_p": "p.Pro413Pro",
"transcript": "ENST00000884318.1",
"protein_id": "ENSP00000554377.1",
"transcript_support_level": null,
"aa_start": 413,
"aa_end": null,
"aa_length": 700,
"cds_start": 1239,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884318.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1203G>T",
"hgvs_p": "p.Pro401Pro",
"transcript": "ENST00000914266.1",
"protein_id": "ENSP00000584325.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 688,
"cds_start": 1203,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914266.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1203G>T",
"hgvs_p": "p.Pro401Pro",
"transcript": "ENST00000914268.1",
"protein_id": "ENSP00000584327.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 688,
"cds_start": 1203,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914268.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS1",
"gene_hgnc_id": 5163,
"hgvs_c": "c.1203G>T",
"hgvs_p": "p.Pro401Pro",
"transcript": "ENST00000963959.1",
"protein_id": "ENSP00000634018.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 688,
"cds_start": 1203,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963959.1"
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"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
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"phylop100way_prediction": "Benign",
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"spliceai_max_prediction": "Benign",
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"apogee2_prediction": null,
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"acmg_score": -6,
"acmg_classification": "Likely_benign",
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"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_000195.5",
"gene_symbol": "HPS1",
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"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
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"hgvs_p": "p.Pro413Pro"
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{
"score": -5,
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"criteria": [
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"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000699159.1",
"gene_symbol": "ENSG00000289758",
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"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*598G>T",
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}
],
"clinvar_disease": "Hermansky-Pudlak syndrome 1,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not specified|not provided|Hermansky-Pudlak syndrome 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}