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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: 1-52948080-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=52948080&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 52948080,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000371514.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "NM_002979.5",
"protein_id": "NP_002970.2",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 547,
"cds_start": 199,
"cds_end": null,
"cds_length": 1644,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2759,
"mane_select": "ENST00000371514.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "ENST00000371514.8",
"protein_id": "ENSP00000360569.3",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 547,
"cds_start": 199,
"cds_end": null,
"cds_length": 1644,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2759,
"mane_select": "NM_002979.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "ENST00000371509.8",
"protein_id": "ENSP00000360564.4",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 503,
"cds_start": 199,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 310,
"cdna_end": null,
"cdna_length": 1889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "ENST00000371513.9",
"protein_id": "ENSP00000360568.5",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 322,
"cds_start": 199,
"cds_end": null,
"cds_length": 969,
"cdna_start": 278,
"cdna_end": null,
"cdna_length": 2003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "NM_001193600.2",
"protein_id": "NP_001180529.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 503,
"cds_start": 199,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2627,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.-45G>A",
"hgvs_p": null,
"transcript": "NM_001193617.2",
"protein_id": "NP_001180546.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.-45G>A",
"hgvs_p": null,
"transcript": "ENST00000528311.5",
"protein_id": "ENSP00000434132.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "NM_001330587.2",
"protein_id": "NP_001317516.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 366,
"cds_start": 199,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "NM_001007098.3",
"protein_id": "NP_001007099.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 322,
"cds_start": 199,
"cds_end": null,
"cds_length": 969,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.121G>A",
"hgvs_p": "p.Gly41Ser",
"transcript": "ENST00000529363.2",
"protein_id": "ENSP00000431279.2",
"transcript_support_level": 5,
"aa_start": 41,
"aa_end": null,
"aa_length": 238,
"cds_start": 121,
"cds_end": null,
"cds_length": 718,
"cdna_start": 123,
"cdna_end": null,
"cdna_length": 720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "XM_005271103.5",
"protein_id": "XP_005271160.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 463,
"cds_start": 199,
"cds_end": null,
"cds_length": 1392,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "XM_047427504.1",
"protein_id": "XP_047283460.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 463,
"cds_start": 199,
"cds_end": null,
"cds_length": 1392,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 5213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "XM_011541935.3",
"protein_id": "XP_011540237.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 399,
"cds_start": 199,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 6317,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "XM_047427506.1",
"protein_id": "XP_047283462.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 399,
"cds_start": 199,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 4977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "XM_047427507.1",
"protein_id": "XP_047283463.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 399,
"cds_start": 199,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 4986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser",
"transcript": "XM_047427508.1",
"protein_id": "XP_047283464.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 355,
"cds_start": 199,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2935,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "n.199G>A",
"hgvs_p": null,
"transcript": "ENST00000478631.6",
"protein_id": "ENSP00000435194.1",
"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": 5204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "n.216G>A",
"hgvs_p": null,
"transcript": "ENST00000528809.1",
"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": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.-45G>A",
"hgvs_p": null,
"transcript": "NM_001193617.2",
"protein_id": "NP_001180546.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.-45G>A",
"hgvs_p": null,
"transcript": "ENST00000528311.5",
"protein_id": "ENSP00000434132.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1896,
"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": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.128-2675G>A",
"hgvs_p": null,
"transcript": "NM_001193599.2",
"protein_id": "NP_001180528.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 523,
"cds_start": -4,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2687,
"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": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"hgvs_c": "c.128-2675G>A",
"hgvs_p": null,
"transcript": "ENST00000407246.6",
"protein_id": "ENSP00000384569.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 523,
"cds_start": -4,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCP2",
"gene_hgnc_id": 10606,
"dbsnp": "rs1553143461",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8208447694778442,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9980000257492065,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.814,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3866,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.026,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.83,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.9999921825084,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000371514.8",
"gene_symbol": "SCP2",
"hgnc_id": 10606,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.199G>A",
"hgvs_p": "p.Gly67Ser"
}
],
"clinvar_disease": "Leukodystrophy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Leukodystrophy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}