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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: 5-140677924-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=140677924&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 140677924,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002109.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp",
"transcript": "NM_002109.6",
"protein_id": "NP_002100.2",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 509,
"cds_start": 614,
"cds_end": null,
"cds_length": 1530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000504156.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002109.6"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp",
"transcript": "ENST00000504156.7",
"protein_id": "ENSP00000425634.1",
"transcript_support_level": 1,
"aa_start": 205,
"aa_end": null,
"aa_length": 509,
"cds_start": 614,
"cds_end": null,
"cds_length": 1530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002109.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504156.7"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Gly185Asp",
"transcript": "ENST00000457527.6",
"protein_id": "ENSP00000387893.2",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 489,
"cds_start": 554,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457527.6"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.731G>A",
"hgvs_p": "p.Gly244Asp",
"transcript": "ENST00000942727.1",
"protein_id": "ENSP00000612786.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 548,
"cds_start": 731,
"cds_end": null,
"cds_length": 1647,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942727.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp",
"transcript": "ENST00000942728.1",
"protein_id": "ENSP00000612787.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 513,
"cds_start": 614,
"cds_end": null,
"cds_length": 1542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942728.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp",
"transcript": "ENST00000507746.7",
"protein_id": "ENSP00000425889.2",
"transcript_support_level": 5,
"aa_start": 205,
"aa_end": null,
"aa_length": 512,
"cds_start": 614,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507746.7"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp",
"transcript": "ENST00000675204.1",
"protein_id": "ENSP00000501643.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 511,
"cds_start": 614,
"cds_end": null,
"cds_length": 1536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675204.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp",
"transcript": "ENST00000937417.1",
"protein_id": "ENSP00000607476.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 507,
"cds_start": 614,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937417.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Gly185Asp",
"transcript": "ENST00000937418.1",
"protein_id": "ENSP00000607477.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 492,
"cds_start": 554,
"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": "ENST00000937418.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Gly185Asp",
"transcript": "NM_001258041.3",
"protein_id": "NP_001244970.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 489,
"cds_start": 554,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001258041.3"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Gly185Asp",
"transcript": "ENST00000942725.1",
"protein_id": "ENSP00000612784.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 489,
"cds_start": 554,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942725.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.527G>A",
"hgvs_p": "p.Gly176Asp",
"transcript": "NM_001289094.2",
"protein_id": "NP_001276023.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 480,
"cds_start": 527,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001289094.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp",
"transcript": "ENST00000675366.1",
"protein_id": "ENSP00000501747.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 470,
"cds_start": 614,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675366.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.494G>A",
"hgvs_p": "p.Gly165Asp",
"transcript": "NM_001258040.3",
"protein_id": "NP_001244969.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 469,
"cds_start": 494,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001258040.3"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.494G>A",
"hgvs_p": "p.Gly165Asp",
"transcript": "ENST00000438307.6",
"protein_id": "ENSP00000411511.2",
"transcript_support_level": 2,
"aa_start": 165,
"aa_end": null,
"aa_length": 469,
"cds_start": 494,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000438307.6"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.488G>A",
"hgvs_p": "p.Gly163Asp",
"transcript": "ENST00000937419.1",
"protein_id": "ENSP00000607478.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 467,
"cds_start": 488,
"cds_end": null,
"cds_length": 1404,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937419.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.434G>A",
"hgvs_p": "p.Gly145Asp",
"transcript": "NM_001258042.3",
"protein_id": "NP_001244971.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 449,
"cds_start": 434,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001258042.3"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.434G>A",
"hgvs_p": "p.Gly145Asp",
"transcript": "ENST00000307633.7",
"protein_id": "ENSP00000304668.3",
"transcript_support_level": 2,
"aa_start": 145,
"aa_end": null,
"aa_length": 449,
"cds_start": 434,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307633.7"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.407G>A",
"hgvs_p": "p.Gly136Asp",
"transcript": "ENST00000675698.1",
"protein_id": "ENSP00000501581.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 440,
"cds_start": 407,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675698.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.392G>A",
"hgvs_p": "p.Gly131Asp",
"transcript": "ENST00000937415.1",
"protein_id": "ENSP00000607474.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 438,
"cds_start": 392,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937415.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.392G>A",
"hgvs_p": "p.Gly131Asp",
"transcript": "NM_001289092.2",
"protein_id": "NP_001276021.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 435,
"cds_start": 392,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001289092.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.392G>A",
"hgvs_p": "p.Gly131Asp",
"transcript": "ENST00000415192.6",
"protein_id": "ENSP00000411085.2",
"transcript_support_level": 2,
"aa_start": 131,
"aa_end": null,
"aa_length": 435,
"cds_start": 392,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415192.6"
},
{
"aa_ref": "G",
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"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "n.*508G>A",
"hgvs_p": null,
"transcript": "ENST00000646229.1",
"protein_id": "ENSP00000495358.1",
"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": "ENST00000646229.1"
}
],
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"dbsnp": "rs147288996",
"frequency_reference_population": 0.0022301495,
"hom_count_reference_population": 15,
"allele_count_reference_population": 3586,
"gnomad_exomes_af": 0.00217506,
"gnomad_genomes_af": 0.00275821,
"gnomad_exomes_ac": 3167,
"gnomad_genomes_ac": 419,
"gnomad_exomes_homalt": 12,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.010127872228622437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.411,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4847,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.568,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002109.6",
"gene_symbol": "HARS1",
"hgnc_id": 4816,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.614G>A",
"hgvs_p": "p.Gly205Asp"
}
],
"clinvar_disease": "Usher syndrome type 3B,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:4",
"phenotype_combined": "Usher syndrome type 3B|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}