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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: 12-100291623-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=100291623&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 100291623,
"ref": "C",
"alt": "T",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "NM_001330256.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "NM_017988.6",
"protein_id": "NP_060458.3",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 929,
"cds_start": 298,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000360820.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017988.6"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000360820.7",
"protein_id": "ENSP00000354061.2",
"transcript_support_level": 1,
"aa_start": 100,
"aa_end": null,
"aa_length": 929,
"cds_start": 298,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017988.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000360820.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.-358C>T",
"hgvs_p": null,
"transcript": "NM_001330256.2",
"protein_id": "NP_001317185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 760,
"cds_start": null,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330256.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.-222C>T",
"hgvs_p": null,
"transcript": "ENST00000548392.5",
"protein_id": "ENSP00000450294.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 75,
"cds_start": null,
"cds_end": null,
"cds_length": 228,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548392.5"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000930683.1",
"protein_id": "ENSP00000600742.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 952,
"cds_start": 298,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930683.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "NM_001330253.2",
"protein_id": "NP_001317182.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 933,
"cds_start": 298,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330253.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "NM_001330254.2",
"protein_id": "NP_001317183.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 933,
"cds_start": 298,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330254.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000635101.1",
"protein_id": "ENSP00000489123.1",
"transcript_support_level": 5,
"aa_start": 100,
"aa_end": null,
"aa_length": 933,
"cds_start": 298,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635101.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "NM_001317784.2",
"protein_id": "NP_001304713.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 929,
"cds_start": 298,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317784.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000872993.1",
"protein_id": "ENSP00000543052.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 929,
"cds_start": 298,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872993.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000872997.1",
"protein_id": "ENSP00000543056.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 929,
"cds_start": 298,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872997.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000872998.1",
"protein_id": "ENSP00000543057.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 929,
"cds_start": 298,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872998.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000951396.1",
"protein_id": "ENSP00000621455.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 928,
"cds_start": 298,
"cds_end": null,
"cds_length": 2787,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951396.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000930682.1",
"protein_id": "ENSP00000600741.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 894,
"cds_start": 298,
"cds_end": null,
"cds_length": 2685,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930682.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000872994.1",
"protein_id": "ENSP00000543053.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 890,
"cds_start": 298,
"cds_end": null,
"cds_length": 2673,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872994.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000872996.1",
"protein_id": "ENSP00000543055.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 890,
"cds_start": 298,
"cds_end": null,
"cds_length": 2673,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872996.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000872995.1",
"protein_id": "ENSP00000543054.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 855,
"cds_start": 298,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872995.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100*",
"transcript": "ENST00000549687.5",
"protein_id": "ENSP00000448366.1",
"transcript_support_level": 2,
"aa_start": 100,
"aa_end": null,
"aa_length": 680,
"cds_start": 298,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549687.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.-358C>T",
"hgvs_p": null,
"transcript": "NM_001330256.2",
"protein_id": "NP_001317185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 760,
"cds_start": null,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330256.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "c.-222C>T",
"hgvs_p": null,
"transcript": "ENST00000548392.5",
"protein_id": "ENSP00000450294.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 75,
"cds_start": null,
"cds_end": null,
"cds_length": 228,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548392.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "n.137C>T",
"hgvs_p": null,
"transcript": "ENST00000549486.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000549486.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"hgvs_c": "n.474C>T",
"hgvs_p": null,
"transcript": "ENST00000550067.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000550067.1"
}
],
"gene_symbol": "SCYL2",
"gene_hgnc_id": 19286,
"dbsnp": "rs1474619680",
"frequency_reference_population": 0.0000012502798,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.9085e-7,
"gnomad_genomes_af": 0.00000657246,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6000000238418579,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.375,
"phylop100way_prediction": "Benign",
"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": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001330256.2",
"gene_symbol": "SCYL2",
"hgnc_id": 19286,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-358C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}