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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: X-131274771-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=131274771&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 131274771,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000361420.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3579C>T",
"hgvs_p": "p.Val1193Val",
"transcript": "NM_001555.5",
"protein_id": "NP_001546.2",
"transcript_support_level": null,
"aa_start": 1193,
"aa_end": null,
"aa_length": 1336,
"cds_start": 3579,
"cds_end": null,
"cds_length": 4011,
"cdna_start": 3739,
"cdna_end": null,
"cdna_length": 4461,
"mane_select": "ENST00000361420.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3579C>T",
"hgvs_p": "p.Val1193Val",
"transcript": "ENST00000361420.8",
"protein_id": "ENSP00000355010.3",
"transcript_support_level": 1,
"aa_start": 1193,
"aa_end": null,
"aa_length": 1336,
"cds_start": 3579,
"cds_end": null,
"cds_length": 4011,
"cdna_start": 3739,
"cdna_end": null,
"cdna_length": 4461,
"mane_select": "NM_001555.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3594C>T",
"hgvs_p": "p.Val1198Val",
"transcript": "ENST00000370903.8",
"protein_id": "ENSP00000359940.3",
"transcript_support_level": 1,
"aa_start": 1198,
"aa_end": null,
"aa_length": 1341,
"cds_start": 3594,
"cds_end": null,
"cds_length": 4026,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3552C>T",
"hgvs_p": "p.Val1184Val",
"transcript": "ENST00000370910.5",
"protein_id": "ENSP00000359947.1",
"transcript_support_level": 1,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3552,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3684,
"cdna_end": null,
"cdna_length": 4406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3594C>T",
"hgvs_p": "p.Val1198Val",
"transcript": "NM_001170961.2",
"protein_id": "NP_001164432.1",
"transcript_support_level": null,
"aa_start": 1198,
"aa_end": null,
"aa_length": 1341,
"cds_start": 3594,
"cds_end": null,
"cds_length": 4026,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3594C>T",
"hgvs_p": "p.Val1198Val",
"transcript": "NM_001438811.1",
"protein_id": "NP_001425740.1",
"transcript_support_level": null,
"aa_start": 1198,
"aa_end": null,
"aa_length": 1341,
"cds_start": 3594,
"cds_end": null,
"cds_length": 4026,
"cdna_start": 3775,
"cdna_end": null,
"cdna_length": 4497,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3579C>T",
"hgvs_p": "p.Val1193Val",
"transcript": "NM_001438812.1",
"protein_id": "NP_001425741.1",
"transcript_support_level": null,
"aa_start": 1193,
"aa_end": null,
"aa_length": 1336,
"cds_start": 3579,
"cds_end": null,
"cds_length": 4011,
"cdna_start": 3760,
"cdna_end": null,
"cdna_length": 4482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3579C>T",
"hgvs_p": "p.Val1193Val",
"transcript": "NM_001438813.1",
"protein_id": "NP_001425742.1",
"transcript_support_level": null,
"aa_start": 1193,
"aa_end": null,
"aa_length": 1336,
"cds_start": 3579,
"cds_end": null,
"cds_length": 4011,
"cdna_start": 3756,
"cdna_end": null,
"cdna_length": 4478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3579C>T",
"hgvs_p": "p.Val1193Val",
"transcript": "ENST00000651556.1",
"protein_id": "ENSP00000498789.1",
"transcript_support_level": null,
"aa_start": 1193,
"aa_end": null,
"aa_length": 1336,
"cds_start": 3579,
"cds_end": null,
"cds_length": 4011,
"cdna_start": 3762,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3552C>T",
"hgvs_p": "p.Val1184Val",
"transcript": "NM_001170962.2",
"protein_id": "NP_001164433.1",
"transcript_support_level": null,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3552,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3712,
"cdna_end": null,
"cdna_length": 4434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3552C>T",
"hgvs_p": "p.Val1184Val",
"transcript": "ENST00000370904.6",
"protein_id": "ENSP00000359941.1",
"transcript_support_level": 2,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3552,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 4696,
"cdna_end": null,
"cdna_length": 5413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3345C>T",
"hgvs_p": "p.Val1115Val",
"transcript": "NM_001438814.1",
"protein_id": "NP_001425743.1",
"transcript_support_level": null,
"aa_start": 1115,
"aa_end": null,
"aa_length": 1258,
"cds_start": 3345,
"cds_end": null,
"cds_length": 3777,
"cdna_start": 3505,
"cdna_end": null,
"cdna_length": 4227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3330C>T",
"hgvs_p": "p.Val1110Val",
"transcript": "NM_001438815.1",
"protein_id": "NP_001425744.1",
"transcript_support_level": null,
"aa_start": 1110,
"aa_end": null,
"aa_length": 1253,
"cds_start": 3330,
"cds_end": null,
"cds_length": 3762,
"cdna_start": 3490,
"cdna_end": null,
"cdna_length": 4212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3291C>T",
"hgvs_p": "p.Val1097Val",
"transcript": "ENST00000652189.1",
"protein_id": "ENSP00000498607.1",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3291,
"cds_end": null,
"cds_length": 3723,
"cdna_start": 3472,
"cdna_end": null,
"cdna_length": 4159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.564C>T",
"hgvs_p": "p.Val188Val",
"transcript": "ENST00000650945.1",
"protein_id": "ENSP00000498530.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 277,
"cds_start": 564,
"cds_end": null,
"cds_length": 836,
"cdna_start": 566,
"cdna_end": null,
"cdna_length": 838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.114C>T",
"hgvs_p": "p.Val38Val",
"transcript": "ENST00000651402.1",
"protein_id": "ENSP00000498744.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 181,
"cds_start": 114,
"cds_end": null,
"cds_length": 546,
"cdna_start": 116,
"cdna_end": null,
"cdna_length": 730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3594C>T",
"hgvs_p": "p.Val1198Val",
"transcript": "XM_047442085.1",
"protein_id": "XP_047298041.1",
"transcript_support_level": null,
"aa_start": 1198,
"aa_end": null,
"aa_length": 1341,
"cds_start": 3594,
"cds_end": null,
"cds_length": 4026,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 4476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.3018C>T",
"hgvs_p": "p.Val1006Val",
"transcript": "XM_011531334.3",
"protein_id": "XP_011529636.1",
"transcript_support_level": null,
"aa_start": 1006,
"aa_end": null,
"aa_length": 1149,
"cds_start": 3018,
"cds_end": null,
"cds_length": 3450,
"cdna_start": 3178,
"cdna_end": null,
"cdna_length": 3900,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "n.1981C>T",
"hgvs_p": null,
"transcript": "ENST00000651526.1",
"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": 2445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"hgvs_c": "c.149-5C>T",
"hgvs_p": null,
"transcript": "ENST00000650730.1",
"protein_id": "ENSP00000498518.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 51,
"cds_start": -4,
"cds_end": null,
"cds_length": 157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287806",
"gene_hgnc_id": null,
"hgvs_c": "n.560+55298G>A",
"hgvs_p": null,
"transcript": "ENST00000773800.1",
"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": 732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IGSF1",
"gene_hgnc_id": 5948,
"dbsnp": "rs6529473",
"frequency_reference_population": 0.26668558,
"hom_count_reference_population": 141580,
"allele_count_reference_population": 322261,
"gnomad_exomes_af": 0.263457,
"gnomad_genomes_af": 0.298731,
"gnomad_exomes_ac": 289224,
"gnomad_genomes_ac": 33037,
"gnomad_exomes_homalt": 30484,
"gnomad_genomes_homalt": 4060,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5699999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.3100000023841858,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.731,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.31,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000361420.8",
"gene_symbol": "IGSF1",
"hgnc_id": 5948,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3579C>T",
"hgvs_p": "p.Val1193Val"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000773800.1",
"gene_symbol": "ENSG00000287806",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.560+55298G>A",
"hgvs_p": null
}
],
"clinvar_disease": "X-linked central congenital hypothyroidism with late-onset testicular enlargement,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|not provided|X-linked central congenital hypothyroidism with late-onset testicular enlargement",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}