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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: 2-227699195-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227699195&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227699195,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_025243.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "NM_025243.4",
"protein_id": "NP_079519.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000644224.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025243.4"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000644224.2",
"protein_id": "ENSP00000495385.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_025243.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644224.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000258403.8",
"protein_id": "ENSP00000258403.3",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258403.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "n.*545G>A",
"hgvs_p": null,
"transcript": "ENST00000425817.6",
"protein_id": "ENSP00000397393.2",
"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": "ENST00000425817.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "n.*545G>A",
"hgvs_p": null,
"transcript": "ENST00000425817.6",
"protein_id": "ENSP00000397393.2",
"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": "ENST00000425817.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.724G>A",
"hgvs_p": "p.Val242Ile",
"transcript": "ENST00000855519.1",
"protein_id": "ENSP00000525578.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 564,
"cds_start": 724,
"cds_end": null,
"cds_length": 1695,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855519.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.556G>A",
"hgvs_p": "p.Val186Ile",
"transcript": "ENST00000646591.1",
"protein_id": "ENSP00000496701.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 508,
"cds_start": 556,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646591.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "NM_001371411.1",
"protein_id": "NP_001358340.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371411.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "NM_001371412.1",
"protein_id": "NP_001358341.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371412.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000855517.1",
"protein_id": "ENSP00000525576.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855517.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000855518.1",
"protein_id": "ENSP00000525577.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855518.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000958931.1",
"protein_id": "ENSP00000628990.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958931.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000958932.1",
"protein_id": "ENSP00000628991.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958932.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000958933.1",
"protein_id": "ENSP00000628992.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958933.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000958934.1",
"protein_id": "ENSP00000628993.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958934.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000958936.1",
"protein_id": "ENSP00000628995.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958936.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000958937.1",
"protein_id": "ENSP00000628996.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958937.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile",
"transcript": "ENST00000958938.1",
"protein_id": "ENSP00000628997.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958938.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.508G>A",
"hgvs_p": "p.Val170Ile",
"transcript": "NM_001371413.1",
"protein_id": "NP_001358342.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 492,
"cds_start": 508,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371413.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.508G>A",
"hgvs_p": "p.Val170Ile",
"transcript": "NM_001371414.1",
"protein_id": "NP_001358343.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 492,
"cds_start": 508,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001371414.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.556G>A",
"hgvs_p": "p.Val186Ile",
"transcript": "XM_047445927.1",
"protein_id": "XP_047301883.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 508,
"cds_start": 556,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445927.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC19A3",
"gene_hgnc_id": 16266,
"hgvs_c": "c.259+261G>A",
"hgvs_p": null,
"transcript": "ENST00000958935.1",
"protein_id": "ENSP00000628994.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 256,
"cds_start": null,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
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"mane_select": null,
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],
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"computational_score_selected": 0.004443705081939697,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.197,
"revel_prediction": "Benign",
"alphamissense_score": 0.0863,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.338,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": -18,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 20,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_025243.4",
"gene_symbol": "SLC19A3",
"hgnc_id": 16266,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Val174Ile"
}
],
"clinvar_disease": "Biotin-responsive basal ganglia disease,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|not provided|Biotin-responsive basal ganglia disease",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}