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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: 19-12899485-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12899485&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12899485,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000222214.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Ala421Thr",
"transcript": "NM_000159.4",
"protein_id": "NP_000150.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
"aa_length": 438,
"cds_start": 1261,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 1338,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": "ENST00000222214.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Ala421Thr",
"transcript": "ENST00000222214.10",
"protein_id": "ENSP00000222214.4",
"transcript_support_level": 1,
"aa_start": 421,
"aa_end": null,
"aa_length": 438,
"cds_start": 1261,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 1338,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": "NM_000159.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Ala421Thr",
"transcript": "ENST00000591470.5",
"protein_id": "ENSP00000466845.1",
"transcript_support_level": 1,
"aa_start": 421,
"aa_end": null,
"aa_length": 438,
"cds_start": 1261,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 1406,
"cdna_end": null,
"cdna_length": 1867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYCE2",
"gene_hgnc_id": 27411,
"hgvs_c": "c.613-100C>T",
"hgvs_p": null,
"transcript": "NM_001105578.2",
"protein_id": "NP_001099048.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": -4,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1248,
"mane_select": "ENST00000293695.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYCE2",
"gene_hgnc_id": 27411,
"hgvs_c": "c.613-100C>T",
"hgvs_p": null,
"transcript": "ENST00000293695.8",
"protein_id": "ENSP00000293695.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": -4,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1248,
"mane_select": "NM_001105578.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1309G>A",
"hgvs_p": "p.Ala437Thr",
"transcript": "ENST00000587072.2",
"protein_id": "ENSP00000468584.2",
"transcript_support_level": 5,
"aa_start": 437,
"aa_end": null,
"aa_length": 454,
"cds_start": 1309,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1369,
"cdna_end": null,
"cdna_length": 1883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1234G>A",
"hgvs_p": "p.Ala412Thr",
"transcript": "ENST00000714075.1",
"protein_id": "ENSP00000519366.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 429,
"cds_start": 1234,
"cds_end": null,
"cds_length": 1290,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 1771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1225G>A",
"hgvs_p": "p.Ala409Thr",
"transcript": "ENST00000588905.6",
"protein_id": "ENSP00000465770.2",
"transcript_support_level": 5,
"aa_start": 409,
"aa_end": null,
"aa_length": 426,
"cds_start": 1225,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 1786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1135G>A",
"hgvs_p": "p.Ala379Thr",
"transcript": "ENST00000714072.1",
"protein_id": "ENSP00000519363.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 396,
"cds_start": 1135,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1201,
"cdna_end": null,
"cdna_length": 1414,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1591G>A",
"hgvs_p": null,
"transcript": "ENST00000585420.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 1730,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.*752G>A",
"hgvs_p": null,
"transcript": "ENST00000589039.6",
"protein_id": "ENSP00000465618.1",
"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": 1789,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.*701G>A",
"hgvs_p": null,
"transcript": "ENST00000590530.5",
"protein_id": "ENSP00000468452.1",
"transcript_support_level": 2,
"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": 1871,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1571G>A",
"hgvs_p": null,
"transcript": "ENST00000591043.1",
"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": 1764,
"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": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1261G>A",
"hgvs_p": null,
"transcript": "ENST00000714074.1",
"protein_id": "ENSP00000519365.1",
"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,
"cdna_end": null,
"cdna_length": 3178,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1424G>A",
"hgvs_p": null,
"transcript": "NR_102316.1",
"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": 1938,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1642G>A",
"hgvs_p": null,
"transcript": "NR_102317.1",
"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,
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"cdna_length": 2156,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.*752G>A",
"hgvs_p": null,
"transcript": "ENST00000589039.6",
"protein_id": "ENSP00000465618.1",
"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": 1789,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.*701G>A",
"hgvs_p": null,
"transcript": "ENST00000590530.5",
"protein_id": "ENSP00000468452.1",
"transcript_support_level": 2,
"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": 1871,
"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": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1622G>A",
"hgvs_p": null,
"transcript": "ENST00000714069.1",
"protein_id": "ENSP00000519360.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 522,
"cds_start": -4,
"cds_end": null,
"cds_length": 1569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1932,
"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": 14,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1622G>A",
"hgvs_p": null,
"transcript": "ENST00000714068.1",
"protein_id": "ENSP00000519359.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 480,
"cds_start": -4,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1917,
"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": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1622G>A",
"hgvs_p": null,
"transcript": "ENST00000591050.2",
"protein_id": "ENSP00000467735.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 446,
"cds_start": -4,
"cds_end": null,
"cds_length": 1341,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2484,
"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": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1622G>A",
"hgvs_p": null,
"transcript": "ENST00000714070.1",
"protein_id": "ENSP00000519361.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 439,
"cds_start": -4,
"cds_end": null,
"cds_length": 1320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1823,
"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": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1244-215G>A",
"hgvs_p": null,
"transcript": "NM_013976.5",
"protein_id": "NP_039663.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 428,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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{
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{
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{
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{
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"upstream_gene_variant"
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}
],
"gene_symbol": "GCDH",
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"dbsnp": "rs151201155",
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"hom_count_reference_population": 1,
"allele_count_reference_population": 200,
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"gnomad_genomes_ac": 83,
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"gnomad_genomes_homalt": 1,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06658238172531128,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.904,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.169,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.48,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.882,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.05,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM5,PP3,PP5,BP4",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM5",
"PP3",
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000222214.10",
"gene_symbol": "GCDH",
"hgnc_id": 4189,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1261G>A",
"hgvs_p": "p.Ala421Thr"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PP3",
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000293695.8",
"gene_symbol": "SYCE2",
"hgnc_id": 27411,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.613-100C>T",
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}
],
"clinvar_disease": " type 1,Glutaric aciduria,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:6 LP:1 US:1 O:1",
"phenotype_combined": "not provided|Glutaric aciduria, type 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}