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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: 6-5545248-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=5545248&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 5545248,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000274680.9",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_006567.5",
"protein_id": "NP_006558.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1142,
"cdna_end": null,
"cdna_length": 1679,
"mane_select": "ENST00000274680.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "ENST00000274680.9",
"protein_id": "ENSP00000274680.4",
"transcript_support_level": 1,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1142,
"cdna_end": null,
"cdna_length": 1679,
"mane_select": "NM_006567.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "ENST00000324331.10",
"protein_id": "ENSP00000316335.5",
"transcript_support_level": 1,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1309,
"cdna_end": null,
"cdna_length": 1692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_001318872.2",
"protein_id": "NP_001305801.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 1883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_001374875.1",
"protein_id": "NP_001361804.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1600,
"cdna_end": null,
"cdna_length": 2137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_001374876.1",
"protein_id": "NP_001361805.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 1743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_001374877.1",
"protein_id": "NP_001361806.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1664,
"cdna_end": null,
"cdna_length": 2201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_001374878.1",
"protein_id": "NP_001361807.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1379,
"cdna_end": null,
"cdna_length": 1916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_001374879.1",
"protein_id": "NP_001361808.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1231,
"cdna_end": null,
"cdna_length": 1768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "NM_001375257.1",
"protein_id": "NP_001362186.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 451,
"cds_start": 973,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1224,
"cdna_end": null,
"cdna_length": 1761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.841G>T",
"hgvs_p": "p.Asp281Tyr",
"transcript": "NM_001375258.1",
"protein_id": "NP_001362187.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 407,
"cds_start": 841,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 1010,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.277G>T",
"hgvs_p": "p.Asp93Tyr",
"transcript": "NM_001375259.1",
"protein_id": "NP_001362188.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 219,
"cds_start": 277,
"cds_end": null,
"cds_length": 660,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 1046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.277G>T",
"hgvs_p": "p.Asp93Tyr",
"transcript": "NM_001375260.1",
"protein_id": "NP_001362189.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 219,
"cds_start": 277,
"cds_end": null,
"cds_length": 660,
"cdna_start": 765,
"cdna_end": null,
"cdna_length": 1302,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "XM_047418086.1",
"protein_id": "XP_047274042.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
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"cds_start": 973,
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"cdna_start": 1014,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "D",
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "XM_011514247.4",
"protein_id": "XP_011512549.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 439,
"cds_start": 973,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1142,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "XM_011514248.4",
"protein_id": "XP_011512550.1",
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"aa_end": null,
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"cds_start": 973,
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"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr",
"transcript": "XM_011514249.3",
"protein_id": "XP_011512551.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 412,
"cds_start": 973,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1142,
"cdna_end": null,
"cdna_length": 25431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "n.973G>T",
"hgvs_p": null,
"transcript": "ENST00000648580.1",
"protein_id": "ENSP00000497889.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 3884,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "n.*18G>T",
"hgvs_p": null,
"transcript": "XR_007059196.1",
"protein_id": null,
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"aa_start": null,
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"aa_length": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "n.*18G>T",
"hgvs_p": null,
"transcript": "XR_007059197.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1839,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "n.*18G>T",
"hgvs_p": null,
"transcript": "XR_007059198.1",
"protein_id": null,
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"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"hgvs_c": "n.*18G>T",
"hgvs_p": null,
"transcript": "XR_926027.4",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FARS2",
"gene_hgnc_id": 21062,
"dbsnp": "rs764427452",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8789767026901245,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.365,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2785,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.399,
"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_pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000274680.9",
"gene_symbol": "FARS2",
"hgnc_id": 21062,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.973G>T",
"hgvs_p": "p.Asp325Tyr"
}
],
"clinvar_disease": "Combined oxidative phosphorylation defect type 14",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Combined oxidative phosphorylation defect type 14",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}