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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: 3-39066559-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=39066559&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 39066559,
"ref": "T",
"alt": "G",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "NM_001346227.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.280T>G",
"hgvs_p": "p.Ser94Ala",
"transcript": "NM_020839.4",
"protein_id": "NP_065890.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 677,
"cds_start": 280,
"cds_end": null,
"cds_length": 2034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000302313.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020839.4"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.280T>G",
"hgvs_p": "p.Ser94Ala",
"transcript": "ENST00000302313.10",
"protein_id": "ENSP00000307491.5",
"transcript_support_level": 1,
"aa_start": 94,
"aa_end": null,
"aa_length": 677,
"cds_start": 280,
"cds_end": null,
"cds_length": 2034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020839.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000302313.10"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.280T>G",
"hgvs_p": null,
"transcript": "ENST00000420940.6",
"protein_id": "ENSP00000415963.2",
"transcript_support_level": 1,
"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": "ENST00000420940.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.-116T>G",
"hgvs_p": null,
"transcript": "NM_001346227.2",
"protein_id": "NP_001333156.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 502,
"cds_start": null,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346227.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.280T>G",
"hgvs_p": "p.Ser94Ala",
"transcript": "NM_001346225.2",
"protein_id": "NP_001333154.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 715,
"cds_start": 280,
"cds_end": null,
"cds_length": 2148,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346225.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.280T>G",
"hgvs_p": "p.Ser94Ala",
"transcript": "ENST00000925430.1",
"protein_id": "ENSP00000595489.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 715,
"cds_start": 280,
"cds_end": null,
"cds_length": 2148,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925430.1"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.280T>G",
"hgvs_p": "p.Ser94Ala",
"transcript": "ENST00000881530.1",
"protein_id": "ENSP00000551589.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 643,
"cds_start": 280,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881530.1"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.109T>G",
"hgvs_p": "p.Ser37Ala",
"transcript": "NM_001346226.2",
"protein_id": "NP_001333155.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 620,
"cds_start": 109,
"cds_end": null,
"cds_length": 1863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346226.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.70T>G",
"hgvs_p": "p.Ser24Ala",
"transcript": "NM_001346228.2",
"protein_id": "NP_001333157.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 607,
"cds_start": 70,
"cds_end": null,
"cds_length": 1824,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346228.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.34T>G",
"hgvs_p": "p.Ser12Ala",
"transcript": "NM_001303402.2",
"protein_id": "NP_001290331.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 595,
"cds_start": 34,
"cds_end": null,
"cds_length": 1788,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303402.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"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": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.70T>G",
"hgvs_p": "p.Ser24Ala",
"transcript": "ENST00000441361.1",
"protein_id": "ENSP00000416900.1",
"transcript_support_level": 5,
"aa_start": 24,
"aa_end": null,
"aa_length": 161,
"cds_start": 70,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441361.1"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.280T>G",
"hgvs_p": "p.Ser94Ala",
"transcript": "XM_005265346.5",
"protein_id": "XP_005265403.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 707,
"cds_start": 280,
"cds_end": null,
"cds_length": 2124,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265346.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.-116T>G",
"hgvs_p": null,
"transcript": "NM_001346227.2",
"protein_id": "NP_001333156.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 502,
"cds_start": null,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346227.2"
},
{
"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": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.269-16T>G",
"hgvs_p": null,
"transcript": "NM_001303403.2",
"protein_id": "NP_001290332.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 668,
"cds_start": null,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303403.2"
},
{
"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": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "c.269-16T>G",
"hgvs_p": null,
"transcript": "ENST00000881529.1",
"protein_id": "ENSP00000551588.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 668,
"cds_start": null,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881529.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.*9T>G",
"hgvs_p": null,
"transcript": "ENST00000413099.6",
"protein_id": "ENSP00000388720.2",
"transcript_support_level": 2,
"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": "ENST00000413099.6"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.280T>G",
"hgvs_p": null,
"transcript": "ENST00000423296.6",
"protein_id": "ENSP00000401421.2",
"transcript_support_level": 4,
"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": "ENST00000423296.6"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.*75T>G",
"hgvs_p": null,
"transcript": "ENST00000433841.6",
"protein_id": "ENSP00000406025.2",
"transcript_support_level": 3,
"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": "ENST00000433841.6"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.290T>G",
"hgvs_p": null,
"transcript": "NR_144399.2",
"protein_id": null,
"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": "pseudogene",
"feature": "NR_144399.2"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.290T>G",
"hgvs_p": null,
"transcript": "NR_144400.2",
"protein_id": null,
"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": "pseudogene",
"feature": "NR_144400.2"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.290T>G",
"hgvs_p": null,
"transcript": "NR_144401.2",
"protein_id": null,
"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": "pseudogene",
"feature": "NR_144401.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.*9T>G",
"hgvs_p": null,
"transcript": "ENST00000413099.6",
"protein_id": "ENSP00000388720.2",
"transcript_support_level": 2,
"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": "ENST00000413099.6"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"hgvs_c": "n.*75T>G",
"hgvs_p": null,
"transcript": "ENST00000433841.6",
"protein_id": "ENSP00000406025.2",
"transcript_support_level": 3,
"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": "ENST00000433841.6"
}
],
"gene_symbol": "WDR48",
"gene_hgnc_id": 30914,
"dbsnp": "rs148407227",
"frequency_reference_population": 0.0040621688,
"hom_count_reference_population": 15,
"allele_count_reference_population": 6555,
"gnomad_exomes_af": 0.0042058,
"gnomad_genomes_af": 0.00268454,
"gnomad_exomes_ac": 6146,
"gnomad_genomes_ac": 409,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01631489396095276,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.594,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9014,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.94,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001346227.2",
"gene_symbol": "WDR48",
"hgnc_id": 30914,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-116T>G",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary spastic paraplegia,WDR48-related disorder,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Hereditary spastic paraplegia|not provided|WDR48-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}