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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: 3-10301323-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=10301323&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 10301323,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001136026.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Val303Ile",
"transcript": "NM_183352.3",
"protein_id": "NP_899195.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 322,
"cds_start": 907,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000350697.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_183352.3"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Val303Ile",
"transcript": "ENST00000350697.8",
"protein_id": "ENSP00000312122.4",
"transcript_support_level": 1,
"aa_start": 303,
"aa_end": null,
"aa_length": 322,
"cds_start": 907,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_183352.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000350697.8"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.916G>A",
"hgvs_p": "p.Val306Ile",
"transcript": "ENST00000337354.8",
"protein_id": "ENSP00000336566.4",
"transcript_support_level": 1,
"aa_start": 306,
"aa_end": null,
"aa_length": 325,
"cds_start": 916,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000337354.8"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.865G>A",
"hgvs_p": "p.Val289Ile",
"transcript": "ENST00000397109.7",
"protein_id": "ENSP00000380298.3",
"transcript_support_level": 1,
"aa_start": 289,
"aa_end": null,
"aa_length": 308,
"cds_start": 865,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397109.7"
},
{
"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": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "n.1984G>A",
"hgvs_p": null,
"transcript": "ENST00000479868.6",
"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": "ENST00000479868.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Val349Ile",
"transcript": "NM_001136026.3",
"protein_id": "NP_001129498.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 368,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001136026.3"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Val349Ile",
"transcript": "ENST00000383801.6",
"protein_id": "ENSP00000373312.2",
"transcript_support_level": 2,
"aa_start": 349,
"aa_end": null,
"aa_length": 368,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000383801.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.934G>A",
"hgvs_p": "p.Val312Ile",
"transcript": "ENST00000931946.1",
"protein_id": "ENSP00000602008.1",
"transcript_support_level": null,
"aa_start": 312,
"aa_end": null,
"aa_length": 331,
"cds_start": 934,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931946.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.916G>A",
"hgvs_p": "p.Val306Ile",
"transcript": "NM_030673.4",
"protein_id": "NP_109598.2",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 325,
"cds_start": 916,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_030673.4"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.901G>A",
"hgvs_p": "p.Val301Ile",
"transcript": "ENST00000931945.1",
"protein_id": "ENSP00000602004.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 320,
"cds_start": 901,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931945.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.865G>A",
"hgvs_p": "p.Val289Ile",
"transcript": "NM_001136232.3",
"protein_id": "NP_001129704.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 308,
"cds_start": 865,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001136232.3"
},
{
"aa_ref": "V",
"aa_alt": "I",
"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": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.862G>A",
"hgvs_p": "p.Val288Ile",
"transcript": "ENST00000873983.1",
"protein_id": "ENSP00000544042.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 307,
"cds_start": 862,
"cds_end": null,
"cds_length": 924,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873983.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.847G>A",
"hgvs_p": "p.Val283Ile",
"transcript": "ENST00000873984.1",
"protein_id": "ENSP00000544043.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 302,
"cds_start": 847,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873984.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Val349Ile",
"transcript": "XM_047448687.1",
"protein_id": "XP_047304643.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 368,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448687.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Val349Ile",
"transcript": "XM_047448688.1",
"protein_id": "XP_047304644.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 368,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448688.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.961G>A",
"hgvs_p": "p.Val321Ile",
"transcript": "XM_047448690.1",
"protein_id": "XP_047304646.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 340,
"cds_start": 961,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448690.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.961G>A",
"hgvs_p": "p.Val321Ile",
"transcript": "XM_047448691.1",
"protein_id": "XP_047304647.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 340,
"cds_start": 961,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448691.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.916G>A",
"hgvs_p": "p.Val306Ile",
"transcript": "XM_047448692.1",
"protein_id": "XP_047304648.1",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 325,
"cds_start": 916,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448692.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.916G>A",
"hgvs_p": "p.Val306Ile",
"transcript": "XM_047448693.1",
"protein_id": "XP_047304649.1",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 325,
"cds_start": 916,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448693.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.865G>A",
"hgvs_p": "p.Val289Ile",
"transcript": "XM_047448694.1",
"protein_id": "XP_047304650.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 308,
"cds_start": 865,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448694.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.865G>A",
"hgvs_p": "p.Val289Ile",
"transcript": "XM_047448695.1",
"protein_id": "XP_047304651.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 308,
"cds_start": 865,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448695.1"
},
{
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SEC13",
"gene_hgnc_id": 10697,
"hgvs_c": "c.814-176G>A",
"hgvs_p": null,
"transcript": "ENST00000397117.5",
"protein_id": "ENSP00000380306.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 284,
"cds_start": null,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397117.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
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{
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"biotype": "pseudogene",
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],
"gene_symbol": "SEC13",
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"dbsnp": "rs145428556",
"frequency_reference_population": 0.0000055759665,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000478832,
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"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2422158420085907,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.154,
"revel_prediction": "Benign",
"alphamissense_score": 0.1091,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.034,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
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"pathogenic_score": 2,
"criteria": [
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"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001136026.3",
"gene_symbol": "SEC13",
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"effects": [
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],
"inheritance_mode": "AR",
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"hgvs_p": "p.Val349Ile"
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],
"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
}