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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: 6-83170340-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=83170340&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 83170340,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000513973.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "NM_015599.3",
"protein_id": "NP_056414.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 542,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 1593,
"cdna_end": null,
"cdna_length": 6079,
"mane_select": "ENST00000513973.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "ENST00000513973.6",
"protein_id": "ENSP00000424874.1",
"transcript_support_level": 1,
"aa_start": 502,
"aa_end": null,
"aa_length": 542,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 1593,
"cdna_end": null,
"cdna_length": 6079,
"mane_select": "NM_015599.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "ENST00000512866.5",
"protein_id": "ENSP00000421565.1",
"transcript_support_level": 1,
"aa_start": 502,
"aa_end": null,
"aa_length": 566,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 1559,
"cdna_end": null,
"cdna_length": 2013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Asp421Asn",
"transcript": "ENST00000283977.9",
"protein_id": "ENSP00000283977.5",
"transcript_support_level": 5,
"aa_start": 421,
"aa_end": null,
"aa_length": 441,
"cds_start": 1261,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 1388,
"cdna_end": null,
"cdna_length": 2223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1588G>A",
"hgvs_p": "p.Asp530Asn",
"transcript": "NM_001199917.2",
"protein_id": "NP_001186846.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 570,
"cds_start": 1588,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1721,
"cdna_end": null,
"cdna_length": 6207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1588G>A",
"hgvs_p": "p.Asp530Asn",
"transcript": "NM_001367287.1",
"protein_id": "NP_001354216.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 570,
"cds_start": 1588,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1730,
"cdna_end": null,
"cdna_length": 6216,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1588G>A",
"hgvs_p": "p.Asp530Asn",
"transcript": "ENST00000506587.5",
"protein_id": "ENSP00000425809.1",
"transcript_support_level": 2,
"aa_start": 530,
"aa_end": null,
"aa_length": 570,
"cds_start": 1588,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1735,
"cdna_end": null,
"cdna_length": 1971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1588G>A",
"hgvs_p": "p.Asp530Asn",
"transcript": "ENST00000508748.6",
"protein_id": "ENSP00000424865.2",
"transcript_support_level": 5,
"aa_start": 530,
"aa_end": null,
"aa_length": 570,
"cds_start": 1588,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1758,
"cdna_end": null,
"cdna_length": 4518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "NM_001199919.2",
"protein_id": "NP_001186848.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 566,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 1593,
"cdna_end": null,
"cdna_length": 2047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "ENST00000509219.2",
"protein_id": "ENSP00000423389.2",
"transcript_support_level": 5,
"aa_start": 502,
"aa_end": null,
"aa_length": 566,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 1596,
"cdna_end": null,
"cdna_length": 1952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "ENST00000652468.1",
"protein_id": "ENSP00000499112.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 566,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 1752,
"cdna_end": null,
"cdna_length": 2060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "ENST00000507554.2",
"protein_id": "ENSP00000425558.2",
"transcript_support_level": 4,
"aa_start": 502,
"aa_end": null,
"aa_length": 542,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 1620,
"cdna_end": null,
"cdna_length": 2735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"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": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1504G>A",
"hgvs_p": "p.Asp502Asn",
"transcript": "ENST00000698526.1",
"protein_id": "ENSP00000513775.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 527,
"cds_start": 1504,
"cds_end": null,
"cds_length": 1584,
"cdna_start": 1603,
"cdna_end": null,
"cdna_length": 3579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1405G>A",
"hgvs_p": "p.Asp469Asn",
"transcript": "ENST00000652222.2",
"protein_id": "ENSP00000499141.2",
"transcript_support_level": null,
"aa_start": 469,
"aa_end": null,
"aa_length": 509,
"cds_start": 1405,
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"cdna_start": 1494,
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"cdna_length": 1879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1381G>A",
"hgvs_p": "p.Asp461Asn",
"transcript": "NM_001367286.1",
"protein_id": "NP_001354215.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 501,
"cds_start": 1381,
"cds_end": null,
"cds_length": 1506,
"cdna_start": 1470,
"cdna_end": null,
"cdna_length": 5956,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1381G>A",
"hgvs_p": "p.Asp461Asn",
"transcript": "ENST00000650642.1",
"protein_id": "ENSP00000498516.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
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"cds_start": 1381,
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"cdna_start": 1462,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"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": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1405G>A",
"hgvs_p": "p.Asp469Asn",
"transcript": "ENST00000698613.1",
"protein_id": "ENSP00000513839.1",
"transcript_support_level": null,
"aa_start": 469,
"aa_end": null,
"aa_length": 494,
"cds_start": 1405,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 1494,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Asp421Asn",
"transcript": "ENST00000651425.1",
"protein_id": "ENSP00000498986.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
"aa_length": 461,
"cds_start": 1261,
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"cds_length": 1386,
"cdna_start": 1410,
"cdna_end": null,
"cdna_length": 1866,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Asp421Asn",
"transcript": "ENST00000698610.1",
"protein_id": "ENSP00000513837.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
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"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Asp421Asn",
"transcript": "NM_001199918.2",
"protein_id": "NP_001186847.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
"aa_length": 441,
"cds_start": 1261,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1162G>A",
"hgvs_p": "p.Asp388Asn",
"transcript": "ENST00000698608.1",
"protein_id": "ENSP00000513835.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 428,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1287,
"cdna_start": 1268,
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"cdna_length": 4026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
"gene_hgnc_id": 8907,
"hgvs_c": "c.1138G>A",
"hgvs_p": "p.Asp380Asn",
"transcript": "ENST00000616566.5",
"protein_id": "ENSP00000477539.2",
"transcript_support_level": 2,
"aa_start": 380,
"aa_end": null,
"aa_length": 420,
"cds_start": 1138,
"cds_end": null,
"cds_length": 1263,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 2325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGM3",
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}
],
"gene_symbol": "PGM3",
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"dbsnp": "rs267608261",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
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"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5997536778450012,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.262,
"revel_prediction": "Benign",
"alphamissense_score": 0.1725,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.207,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PM5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000513973.6",
"gene_symbol": "PGM3",
"hgnc_id": 8907,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
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"hgvs_p": "p.Asp502Asn"
},
{
"score": 2,
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"pathogenic_score": 2,
"criteria": [
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],
"verdict": "Uncertain_significance",
"transcript": "ENST00000484282.1",
"gene_symbol": "DOP1A",
"hgnc_id": 21194,
"effects": [
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],
"inheritance_mode": "AR",
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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
}