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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: 1-6464394-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=6464394&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 6464394,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000356876.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser",
"transcript": "NM_003790.3",
"protein_id": "NP_003781.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 417,
"cds_start": 523,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 589,
"cdna_end": null,
"cdna_length": 1968,
"mane_select": "ENST00000356876.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser",
"transcript": "ENST00000356876.8",
"protein_id": "ENSP00000349341.3",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 417,
"cds_start": 523,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 589,
"cdna_end": null,
"cdna_length": 1968,
"mane_select": "NM_003790.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser",
"transcript": "ENST00000377782.7",
"protein_id": "ENSP00000367013.3",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 426,
"cds_start": 523,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 591,
"cdna_end": null,
"cdna_length": 1632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser",
"transcript": "ENST00000351959.9",
"protein_id": "ENSP00000337713.5",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 380,
"cds_start": 523,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 591,
"cdna_end": null,
"cdna_length": 1441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Gly130Ser",
"transcript": "ENST00000348333.7",
"protein_id": "ENSP00000314451.3",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 372,
"cds_start": 388,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 388,
"cdna_end": null,
"cdna_length": 1119,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.523G>A",
"hgvs_p": null,
"transcript": "ENST00000414040.6",
"protein_id": "ENSP00000404274.2",
"transcript_support_level": 1,
"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": 1198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.515G>A",
"hgvs_p": null,
"transcript": "ENST00000453341.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.523G>A",
"hgvs_p": null,
"transcript": "ENST00000461703.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.523G>A",
"hgvs_p": null,
"transcript": "ENST00000480393.5",
"protein_id": "ENSP00000434129.1",
"transcript_support_level": 1,
"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": 1706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.523G>A",
"hgvs_p": null,
"transcript": "ENST00000485036.5",
"protein_id": "ENSP00000431554.1",
"transcript_support_level": 1,
"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": 1726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.388G>A",
"hgvs_p": null,
"transcript": "ENST00000502588.5",
"protein_id": "ENSP00000423121.1",
"transcript_support_level": 1,
"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": 952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.523G>A",
"hgvs_p": null,
"transcript": "ENST00000510563.5",
"protein_id": "ENSP00000424071.1",
"transcript_support_level": 1,
"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": 1087,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.160+1046G>A",
"hgvs_p": null,
"transcript": "ENST00000351748.7",
"protein_id": "ENSP00000326762.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": -4,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.328+158G>A",
"hgvs_p": null,
"transcript": "ENST00000502730.5",
"protein_id": "ENSP00000421976.1",
"transcript_support_level": 1,
"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": 838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser",
"transcript": "NM_148965.2",
"protein_id": "NP_683866.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 426,
"cds_start": 523,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 589,
"cdna_end": null,
"cdna_length": 1995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser",
"transcript": "NM_148966.2",
"protein_id": "NP_683867.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 380,
"cds_start": 523,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 589,
"cdna_end": null,
"cdna_length": 1857,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.394G>A",
"hgvs_p": "p.Gly132Ser",
"transcript": "ENST00000647810.1",
"protein_id": "ENSP00000497258.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 373,
"cds_start": 394,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 1770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Gly130Ser",
"transcript": "NM_148967.2",
"protein_id": "NP_683868.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 372,
"cds_start": 388,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 454,
"cdna_end": null,
"cdna_length": 1833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser",
"transcript": "NM_001039664.2",
"protein_id": "NP_001034753.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 181,
"cds_start": 523,
"cds_end": null,
"cds_length": 546,
"cdna_start": 589,
"cdna_end": null,
"cdna_length": 872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.413G>A",
"hgvs_p": null,
"transcript": "ENST00000469691.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.1121G>A",
"hgvs_p": null,
"transcript": "ENST00000513135.5",
"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": 3483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.-75G>A",
"hgvs_p": null,
"transcript": "ENST00000481401.5",
"protein_id": "ENSP00000465381.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 44,
"cds_start": -4,
"cds_end": null,
"cds_length": 136,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 764,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "c.160+1046G>A",
"hgvs_p": null,
"transcript": "NM_148970.2",
"protein_id": "NP_683871.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": -4,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1419,
"mane_select": null,
"mane_plus": null,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"hgvs_c": "n.*173G>A",
"hgvs_p": null,
"transcript": "ENST00000515145.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNFRSF25",
"gene_hgnc_id": 11910,
"dbsnp": "rs776514042",
"frequency_reference_population": 0.00003228482,
"hom_count_reference_population": 0,
"allele_count_reference_population": 52,
"gnomad_exomes_af": 0.0000335984,
"gnomad_genomes_af": 0.0000197029,
"gnomad_exomes_ac": 49,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05066269636154175,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.18,
"revel_prediction": "Benign",
"alphamissense_score": 0.0606,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.092,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000356876.8",
"gene_symbol": "TNFRSF25",
"hgnc_id": 11910,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Gly175Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}