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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: 4-39467592-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=39467592&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 39467592,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000640888.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.683T>C",
"hgvs_p": "p.Leu228Pro",
"transcript": "NM_006859.4",
"protein_id": "NP_006850.2",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 372,
"cds_start": 683,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 3572,
"mane_select": "ENST00000640888.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.683T>C",
"hgvs_p": "p.Leu228Pro",
"transcript": "ENST00000640888.2",
"protein_id": "ENSP00000492260.1",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 372,
"cds_start": 683,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 3572,
"mane_select": "NM_006859.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.683T>C",
"hgvs_p": "p.Leu228Pro",
"transcript": "NM_194451.3",
"protein_id": "NP_919433.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 322,
"cds_start": 683,
"cds_end": null,
"cds_length": 969,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 3460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.683T>C",
"hgvs_p": "p.Leu228Pro",
"transcript": "ENST00000340169.7",
"protein_id": "ENSP00000340676.2",
"transcript_support_level": 5,
"aa_start": 228,
"aa_end": null,
"aa_length": 322,
"cds_start": 683,
"cds_end": null,
"cds_length": 969,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 1485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.569T>C",
"hgvs_p": "p.Leu190Pro",
"transcript": "ENST00000640349.1",
"protein_id": "ENSP00000491477.1",
"transcript_support_level": 5,
"aa_start": 190,
"aa_end": null,
"aa_length": 320,
"cds_start": 569,
"cds_end": null,
"cds_length": 965,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.374T>C",
"hgvs_p": "p.Leu125Pro",
"transcript": "NM_001363700.2",
"protein_id": "NP_001350629.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 269,
"cds_start": 374,
"cds_end": null,
"cds_length": 810,
"cdna_start": 436,
"cdna_end": null,
"cdna_length": 3263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.374T>C",
"hgvs_p": "p.Leu125Pro",
"transcript": "ENST00000261434.8",
"protein_id": "ENSP00000261434.4",
"transcript_support_level": 5,
"aa_start": 125,
"aa_end": null,
"aa_length": 269,
"cds_start": 374,
"cds_end": null,
"cds_length": 810,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 1258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.293T>C",
"hgvs_p": "p.Leu98Pro",
"transcript": "ENST00000513731.6",
"protein_id": "ENSP00000425580.1",
"transcript_support_level": 5,
"aa_start": 98,
"aa_end": null,
"aa_length": 242,
"cds_start": 293,
"cds_end": null,
"cds_length": 729,
"cdna_start": 345,
"cdna_end": null,
"cdna_length": 826,
"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": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.683T>C",
"hgvs_p": null,
"transcript": "ENST00000638422.1",
"protein_id": "ENSP00000491001.1",
"transcript_support_level": 5,
"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": 1776,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*286T>C",
"hgvs_p": null,
"transcript": "ENST00000638430.1",
"protein_id": "ENSP00000491831.1",
"transcript_support_level": 5,
"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": 1237,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*82T>C",
"hgvs_p": null,
"transcript": "ENST00000638816.1",
"protein_id": "ENSP00000492482.1",
"transcript_support_level": 5,
"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": 675,
"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": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*39T>C",
"hgvs_p": null,
"transcript": "ENST00000639422.1",
"protein_id": "ENSP00000491899.1",
"transcript_support_level": 5,
"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": 4115,
"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": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.743T>C",
"hgvs_p": null,
"transcript": "ENST00000640381.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 2259,
"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": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*286T>C",
"hgvs_p": null,
"transcript": "ENST00000640689.1",
"protein_id": "ENSP00000491591.1",
"transcript_support_level": 5,
"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": 2080,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"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": "ENSG00000298383",
"gene_hgnc_id": null,
"hgvs_c": "n.1323A>G",
"hgvs_p": null,
"transcript": "ENST00000755221.1",
"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": 1785,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*286T>C",
"hgvs_p": null,
"transcript": "ENST00000638430.1",
"protein_id": "ENSP00000491831.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"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": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*82T>C",
"hgvs_p": null,
"transcript": "ENST00000638816.1",
"protein_id": "ENSP00000492482.1",
"transcript_support_level": 5,
"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": 675,
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*39T>C",
"hgvs_p": null,
"transcript": "ENST00000639422.1",
"protein_id": "ENSP00000491899.1",
"transcript_support_level": 5,
"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": 4115,
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "n.*286T>C",
"hgvs_p": null,
"transcript": "ENST00000640689.1",
"protein_id": "ENSP00000491591.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.608+2250T>C",
"hgvs_p": null,
"transcript": "NM_001278590.2",
"protein_id": "NP_001265519.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 329,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.608+2250T>C",
"hgvs_p": null,
"transcript": "ENST00000381846.2",
"protein_id": "ENSP00000371270.1",
"transcript_support_level": 3,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.368+2250T>C",
"hgvs_p": null,
"transcript": "ENST00000640672.1",
"protein_id": "ENSP00000492203.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 265,
"cds_start": -4,
"cds_end": null,
"cds_length": 798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "LIAS",
"gene_hgnc_id": 16429,
"hgvs_c": "c.300-2427T>C",
"hgvs_p": null,
"transcript": "ENST00000638451.1",
"protein_id": "ENSP00000491681.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 226,
"cds_start": -4,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LIAS",
"gene_hgnc_id": 16429,
"dbsnp": "rs1553934545",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23869872093200684,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.352,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7726,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.479,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000640888.2",
"gene_symbol": "LIAS",
"hgnc_id": 16429,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.683T>C",
"hgvs_p": "p.Leu228Pro"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000755221.1",
"gene_symbol": "ENSG00000298383",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1323A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Lipoic acid synthetase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Lipoic acid synthetase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}